Chain A, Spike glycoprotein,Foldon chimera
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||
| CoV_Spike_S1-S2_S2 super family | cl40439 | S1/S2 cleavage region and the S2 fusion subunit of coronavirus spike (S) proteins; This model ... |
611-1272 | 0e+00 | ||||||||||
S1/S2 cleavage region and the S2 fusion subunit of coronavirus spike (S) proteins; This model represents the S1/S2 cleavage region and the S2 subunit of the spike (S) glycoprotein from coronavirus (CoVs), including three highly pathogenic human CoVs, Middle East respiratory syndrome coronavirus (MERS-CoV), Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS coronavirus 2 (SARS-CoV-2), also known as a 2019 novel coronavirus (2019-nCoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect S1 and S2. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV, and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP), and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. Notably, SARS-CoV-2 has a functional polybasic (furin) cleavage site through the insertion of PRRAR*SV (* indicates the cleavage site) at the S1/S2 interface, which is absent in SARS-CoV and other SARS-related CoVs. The S1/S2 cleavage region and the S2 fusion subunit play an essential role in viral entry by initiating fusion of the viral and cellular membranes. The actual alignment was detected with superfamily member cd22380: Pssm-ID: 424070 [Multi-domain] Cd Length: 663 Bit Score: 1231.18 E-value: 0e+00
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| HKU1_N5-like_CoV_Spike_S1_RBD | cd21482 | receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1, ... |
294-597 | 0e+00 | ||||||||||
receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1, isolate N5 and isolate N2; This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from human coronavirus (CoV) HKU1, isolates N5 and N2. HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease, and is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs use the C-domain to bind their receptors. Although a protein receptor has not yet been identified for HKU1, antibodies against the C-domain, but not those against the NTD, blocked HKU1 infection of cells, suggesting that the S1 C-domain is the primary HKU1 receptor-binding site. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs, and most likely, for HKU1. : Pssm-ID: 394829 Cd Length: 304 Bit Score: 601.67 E-value: 0e+00
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| MHV-like_Spike_S1_NTD | cd21625 | N-terminal domain of the S1 subunit of the Spike (S) protein from murine hepatitis virus and ... |
2-281 | 5.12e-177 | ||||||||||
N-terminal domain of the S1 subunit of the Spike (S) protein from murine hepatitis virus and related betacoronaviruses in the A lineage; This subfamily contains the N-terminal domain (NTD) of the S1 subunit of the Spike (S) proteins from betacoronaviruses in the embecovirus subgenera (A lineage), including murine hepatitis virus (MHV), human coronavirus (HCoV) HKU1 and OC43, and bovine CoV (BCoV). MHV is the most common viral pathogen in contemporary laboratory mouse colonies manifesting as a primary infection in the upper respiratory tract, while HCoV-HKU1 causes mild yet prevalent respiratory disease in humans. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While most CoVs, including SARS-CoV and MERS-CoV use the C-domain to bind their receptors, several CoVs in the A lineage use the NTD to bind their receptors. MHV binds its protein receptor, mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a), through its S1 NTD. BCoV and HCoV-OC43 recognize a sugar moiety, 5-N-acetyl-9-O-acetylneuraminic acid (Neu5,9Ac2), on cell-surface glycoproteins or glycolipids; this binding is also through the S1 NTD. In addition, the S1 NTD contributes to the Spike trimer interface. : Pssm-ID: 394951 Cd Length: 284 Bit Score: 524.26 E-value: 5.12e-177
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| Fibritin_C super family | cl44324 | Fibritin C-terminal region; This family features sequences bearing similarity to the ... |
1258-1291 | 3.40e-08 | ||||||||||
Fibritin C-terminal region; This family features sequences bearing similarity to the C-terminal portion of the bacteriophage T4 protein fibritin. This protein is responsible for attachment of long tail fibres to virus particle, and forms the 'whiskers' or fibres on the neck of the virion. The region seen in this family contains an N-terminal coiled-coil portion and the C-terminal globular foldon domain (residues 457-486), which is essential for fibritin trimerization and folding. This domain consists of a beta-hairpin; three such hairpins come together in a beta-propeller-like arrangement in the trimer, which is stabilized by hydrogen bonds, salt bridges and hydrophobic interactions. The actual alignment was detected with superfamily member pfam07921: Pssm-ID: 254516 [Multi-domain] Cd Length: 93 Bit Score: 52.46 E-value: 3.40e-08
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| Name | Accession | Description | Interval | E-value | ||||||||||
| HKU1-CoV-like_Spike_SD1-2_S1-S2_S2 | cd22380 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
611-1272 | 0e+00 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from human HKU1 and OC43 coronaviruses and related betacoronaviruses in the A lineage; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the embecovirus subgenus (A lineage), including highly pathogenic human coronaviruses (CoVs), HKU1 and OC43 CoVs, as well as murine hepatitis virus (MHV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of MHV is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411967 [Multi-domain] Cd Length: 663 Bit Score: 1231.18 E-value: 0e+00
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| CoV_S2 | pfam01601 | Coronavirus spike glycoprotein S2; The coronavirus spike glycoprotein forms the characteriztic ... |
773-1265 | 0e+00 | ||||||||||
Coronavirus spike glycoprotein S2; The coronavirus spike glycoprotein forms the characteriztic 'corona' after which the group is named. The Spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 pfam01600 and S2,. The S2 subunit normally contains multiple key components, including one or more fusion peptides (FP), a second proteolytic site (S2') and two conserved heptad repeats (HRs), driving membrane penetration and virus-cell fusion. The HRs can trimerize into a coiled-coil structure built of three HR1-HR2 helical hairpins presenting as a canonical six-helix bundle and drag the virus envelope and the host cell bilayer into close proximity, preparing for fusion to occur. Pssm-ID: 460263 Cd Length: 502 Bit Score: 633.15 E-value: 0e+00
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| HKU1_N5-like_CoV_Spike_S1_RBD | cd21482 | receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1, ... |
294-597 | 0e+00 | ||||||||||
receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1, isolate N5 and isolate N2; This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from human coronavirus (CoV) HKU1, isolates N5 and N2. HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease, and is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs use the C-domain to bind their receptors. Although a protein receptor has not yet been identified for HKU1, antibodies against the C-domain, but not those against the NTD, blocked HKU1 infection of cells, suggesting that the S1 C-domain is the primary HKU1 receptor-binding site. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs, and most likely, for HKU1. Pssm-ID: 394829 Cd Length: 304 Bit Score: 601.67 E-value: 0e+00
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| MHV-like_Spike_S1_NTD | cd21625 | N-terminal domain of the S1 subunit of the Spike (S) protein from murine hepatitis virus and ... |
2-281 | 5.12e-177 | ||||||||||
N-terminal domain of the S1 subunit of the Spike (S) protein from murine hepatitis virus and related betacoronaviruses in the A lineage; This subfamily contains the N-terminal domain (NTD) of the S1 subunit of the Spike (S) proteins from betacoronaviruses in the embecovirus subgenera (A lineage), including murine hepatitis virus (MHV), human coronavirus (HCoV) HKU1 and OC43, and bovine CoV (BCoV). MHV is the most common viral pathogen in contemporary laboratory mouse colonies manifesting as a primary infection in the upper respiratory tract, while HCoV-HKU1 causes mild yet prevalent respiratory disease in humans. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While most CoVs, including SARS-CoV and MERS-CoV use the C-domain to bind their receptors, several CoVs in the A lineage use the NTD to bind their receptors. MHV binds its protein receptor, mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a), through its S1 NTD. BCoV and HCoV-OC43 recognize a sugar moiety, 5-N-acetyl-9-O-acetylneuraminic acid (Neu5,9Ac2), on cell-surface glycoproteins or glycolipids; this binding is also through the S1 NTD. In addition, the S1 NTD contributes to the Spike trimer interface. Pssm-ID: 394951 Cd Length: 284 Bit Score: 524.26 E-value: 5.12e-177
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| bCoV_S1_N | pfam16451 | Betacoronavirus-like spike glycoprotein S1, N-terminal; This entry represents the N-terminal ... |
28-312 | 2.68e-75 | ||||||||||
Betacoronavirus-like spike glycoprotein S1, N-terminal; This entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like domain (NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Either the S1 NTD or S1 RBD, or occasionally both, are involved in binding to host receptors. S1 NTD is located on the side of the spike trimer and mainly recognizes sugar receptors. For many betacoronaviruses (b-CoVs), for example mouse hepatitis virus (MHV), the RBD is located in the NTD. The structure of the MHV S1 NTD showed the same fold as human galectins (galactose-binding lectin), however it does not bind any sugar; instead, it binds to the carcinoembryonic antigen cell-adhesion molecule CEACAM1) through protein-protein interactions. All three CEACAM21a-binding sites in MHV spikes can be fully occupied by CEACAM1a. It has been shown that CEACAM1a binding to the MHV spike weakens the interactions between S1 and S2 and facilitates the proteolysis of the spike protein and dissociation of S1. The homologous bovine CoV (BCov) S1 NTD also possesses a galectin fold but binds to sialic acid-containing moieties on host cell membranes, as does the NTD of three other group A b-Covs, namely human CoV (HCoV) OC43, avian b-CoV, and infectious bronchitis virus (IBV). Despite the S1 NTD of human respiratory b-CoV HKU1 being highly homologous to the NTDs of MHV and bovine CoV, it does not bind to either sugar or human carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) and the RBD is found instead in the S1 RBD domain. Pssm-ID: 465119 Cd Length: 296 Bit Score: 251.95 E-value: 2.68e-75
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| bCoV_S1_RBD | pfam09408 | Betacoronavirus spike glycoprotein S1, receptor binding; This entry represents the receptor ... |
326-483 | 1.22e-30 | ||||||||||
Betacoronavirus spike glycoprotein S1, receptor binding; This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilize both the S1 NTD and S1 RBD for viral entry. SARS-CoV makes use of its S1 RBD to bind to the human angiotensin-converting enzyme 2 (ACE2) as its host receptor. Pssm-ID: 462789 Cd Length: 156 Bit Score: 118.76 E-value: 1.22e-30
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| Fibritin_C | pfam07921 | Fibritin C-terminal region; This family features sequences bearing similarity to the ... |
1258-1291 | 3.40e-08 | ||||||||||
Fibritin C-terminal region; This family features sequences bearing similarity to the C-terminal portion of the bacteriophage T4 protein fibritin. This protein is responsible for attachment of long tail fibres to virus particle, and forms the 'whiskers' or fibres on the neck of the virion. The region seen in this family contains an N-terminal coiled-coil portion and the C-terminal globular foldon domain (residues 457-486), which is essential for fibritin trimerization and folding. This domain consists of a beta-hairpin; three such hairpins come together in a beta-propeller-like arrangement in the trimer, which is stabilized by hydrogen bonds, salt bridges and hydrophobic interactions. Pssm-ID: 254516 [Multi-domain] Cd Length: 93 Bit Score: 52.46 E-value: 3.40e-08
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| wac | PHA02607 | fibritin; Provisional |
1255-1292 | 1.72e-06 | ||||||||||
fibritin; Provisional Pssm-ID: 177432 [Multi-domain] Cd Length: 454 Bit Score: 51.95 E-value: 1.72e-06
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| Name | Accession | Description | Interval | E-value | ||||||||||
| HKU1-CoV-like_Spike_SD1-2_S1-S2_S2 | cd22380 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
611-1272 | 0e+00 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from human HKU1 and OC43 coronaviruses and related betacoronaviruses in the A lineage; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the embecovirus subgenus (A lineage), including highly pathogenic human coronaviruses (CoVs), HKU1 and OC43 CoVs, as well as murine hepatitis virus (MHV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of MHV is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411967 [Multi-domain] Cd Length: 663 Bit Score: 1231.18 E-value: 0e+00
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| betaCoV_Spike_SD1-2_S1-S2_S2 | cd22370 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
611-1272 | 0e+00 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses; This family contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses, including three highly pathogenic human coronaviruses (CoVs), Middle East respiratory syndrome coronavirus (MERS-CoV), Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS coronavirus 2 (SARS-CoV-2), also known as a 2019 novel coronavirus (2019-nCoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411957 [Multi-domain] Cd Length: 667 Bit Score: 1035.51 E-value: 0e+00
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| CoV_S2 | pfam01601 | Coronavirus spike glycoprotein S2; The coronavirus spike glycoprotein forms the characteriztic ... |
773-1265 | 0e+00 | ||||||||||
Coronavirus spike glycoprotein S2; The coronavirus spike glycoprotein forms the characteriztic 'corona' after which the group is named. The Spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 pfam01600 and S2,. The S2 subunit normally contains multiple key components, including one or more fusion peptides (FP), a second proteolytic site (S2') and two conserved heptad repeats (HRs), driving membrane penetration and virus-cell fusion. The HRs can trimerize into a coiled-coil structure built of three HR1-HR2 helical hairpins presenting as a canonical six-helix bundle and drag the virus envelope and the host cell bilayer into close proximity, preparing for fusion to occur. Pssm-ID: 460263 Cd Length: 502 Bit Score: 633.15 E-value: 0e+00
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| HKU1_N5-like_CoV_Spike_S1_RBD | cd21482 | receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1, ... |
294-597 | 0e+00 | ||||||||||
receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1, isolate N5 and isolate N2; This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from human coronavirus (CoV) HKU1, isolates N5 and N2. HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease, and is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs use the C-domain to bind their receptors. Although a protein receptor has not yet been identified for HKU1, antibodies against the C-domain, but not those against the NTD, blocked HKU1 infection of cells, suggesting that the S1 C-domain is the primary HKU1 receptor-binding site. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs, and most likely, for HKU1. Pssm-ID: 394829 Cd Length: 304 Bit Score: 601.67 E-value: 0e+00
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| bat-HKU9-CoV-like_Spike_SD1-2_S1-S2_S2 | cd22381 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
611-1265 | 1.17e-177 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Rousettus bat coronavirus HKU9 and related betacoronaviruses in the D lineage; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the nobecovirus subgenus (D lineage), including Rousettus bat coronavirus HKU9 (Ro-BatCoV HKU9). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411968 [Multi-domain] Cd Length: 731 Bit Score: 543.58 E-value: 1.17e-177
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| MHV-like_Spike_S1_NTD | cd21625 | N-terminal domain of the S1 subunit of the Spike (S) protein from murine hepatitis virus and ... |
2-281 | 5.12e-177 | ||||||||||
N-terminal domain of the S1 subunit of the Spike (S) protein from murine hepatitis virus and related betacoronaviruses in the A lineage; This subfamily contains the N-terminal domain (NTD) of the S1 subunit of the Spike (S) proteins from betacoronaviruses in the embecovirus subgenera (A lineage), including murine hepatitis virus (MHV), human coronavirus (HCoV) HKU1 and OC43, and bovine CoV (BCoV). MHV is the most common viral pathogen in contemporary laboratory mouse colonies manifesting as a primary infection in the upper respiratory tract, while HCoV-HKU1 causes mild yet prevalent respiratory disease in humans. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While most CoVs, including SARS-CoV and MERS-CoV use the C-domain to bind their receptors, several CoVs in the A lineage use the NTD to bind their receptors. MHV binds its protein receptor, mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a), through its S1 NTD. BCoV and HCoV-OC43 recognize a sugar moiety, 5-N-acetyl-9-O-acetylneuraminic acid (Neu5,9Ac2), on cell-surface glycoproteins or glycolipids; this binding is also through the S1 NTD. In addition, the S1 NTD contributes to the Spike trimer interface. Pssm-ID: 394951 Cd Length: 284 Bit Score: 524.26 E-value: 5.12e-177
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| MERS-CoV-like_Spike_SD1-2_S1-S2_S2 | cd22379 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
611-1268 | 1.51e-162 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Middle East respiratory syndrome coronavirus and related betacoronaviruses in the C lineage; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the merbecovirus subgenus (C lineage), including Middle East respiratory syndrome coronavirus (MERS-CoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411966 [Multi-domain] Cd Length: 682 Bit Score: 502.02 E-value: 1.51e-162
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| HKU1_N1_CoV_Spike_S1_RBD | cd21483 | receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1, ... |
294-595 | 1.06e-159 | ||||||||||
receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1, isolate N1; This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from human coronavirus (CoV) HKU1, isolate N1. HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease, and is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs use the C-domain to bind their receptors. Although a protein receptor has not yet been identified for HKU1, antibodies against the C-domain, but not those against the NTD, blocked HKU1 infection of cells, suggesting that the S1 C-domain is the primary HKU1 receptor-binding site. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs, and most likely, for HKU1. Pssm-ID: 394830 Cd Length: 306 Bit Score: 479.99 E-value: 1.06e-159
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| CoV_Spike_S1-S2_S2 | cd21698 | S1/S2 cleavage region and the S2 fusion subunit of coronavirus spike (S) proteins; This model ... |
774-1265 | 3.12e-150 | ||||||||||
S1/S2 cleavage region and the S2 fusion subunit of coronavirus spike (S) proteins; This model represents the S1/S2 cleavage region and the S2 subunit of the spike (S) glycoprotein from coronavirus (CoVs), including three highly pathogenic human CoVs, Middle East respiratory syndrome coronavirus (MERS-CoV), Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS coronavirus 2 (SARS-CoV-2), also known as a 2019 novel coronavirus (2019-nCoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect S1 and S2. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV, and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP), and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. Notably, SARS-CoV-2 has a functional polybasic (furin) cleavage site through the insertion of PRRAR*SV (* indicates the cleavage site) at the S1/S2 interface, which is absent in SARS-CoV and other SARS-related CoVs. The S1/S2 cleavage region and the S2 fusion subunit play an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411955 [Multi-domain] Cd Length: 523 Bit Score: 463.81 E-value: 3.12e-150
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| gammaCoV_Spike_SD1-2_S1-S2_S2 | cd22372 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
601-1265 | 3.68e-139 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from avian infectious bronchitis coronavirus (IBV) and related gammacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from gammacoronaviruses, including avian infectious bronchitis virus, and Beluga whale coronavirus SW1 (whale-CoV SW1). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411959 [Multi-domain] Cd Length: 661 Bit Score: 439.42 E-value: 3.68e-139
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| SARS-CoV-like_Spike_SD1-2_S1-S2_S2 | cd22378 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
613-1265 | 2.23e-134 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from SARS-CoV-2 (COVID-19) and related betacoronaviruses in the B lineage; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the sarbecovirus subgenus (B lineage), including highly pathogenic human CoVs such as Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS-CoV-2 (also known as a 2019 novel coronavirus or 2019-nCoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. Notably, SARS-CoV-2 has a functional polybasic (furin) cleavage site through the insertion of PRRAR*SV (* indicates the cleavage site) at the S1/S2 interface, which is absent in SARS-CoV and other SARS-related coronaviruses. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411965 [Multi-domain] Cd Length: 662 Bit Score: 426.72 E-value: 2.23e-134
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| MHV-like_Spike_S1_RBD | cd21484 | receptor-binding domain of the S1 subunit of the Spike (S) protein from mouse hepatitis virus ... |
294-594 | 6.05e-131 | ||||||||||
receptor-binding domain of the S1 subunit of the Spike (S) protein from mouse hepatitis virus and other rodent coronaviruses; This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from mouse hepatitis virus (MHV) and other rodent coronaviruses. MHV is the most common viral pathogen in contemporary laboratory mouse colonies manifesting as a primary infection in the upper respiratory tract. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). MHV uses mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a) as the receptor; the RBD of MHV is located at the NTD. Most CoVs, such as SARS-CoV and MERS-CoV, use the C-domain to bind their receptors. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs. Pssm-ID: 394831 Cd Length: 264 Bit Score: 402.72 E-value: 6.05e-131
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| HCoV-OC43-like_Spike_S1_RBD | cd21485 | receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus OC43 ... |
294-594 | 1.19e-124 | ||||||||||
receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus OC43 and related proteins; This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from several betacoronaviruses including human coronavirus OC43 (HCoV-OC43) and bovine respiratory coronavirus (BCoV), among others. HCoV-OC43 is of zoonotic origin and is endemic in the human population, causing mild respiratory tract infections and possible severe complications or fatalities in young children, the elderly, and immunocompromised individuals. These viruses are related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs use the C-domain to bind their receptors. It has been reported that HCoV-OC43 uses 9-O-acetyl-sialic acid (9-O-Ac-Sia) as a receptor, which is terminally linked to oligosaccharides decorating glycoproteins and gangliosides at the host cell surface. HCoV-OC43 appears to bind 9-O-Ac-Sia at the NTD. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs. Pssm-ID: 394832 Cd Length: 312 Bit Score: 387.83 E-value: 1.19e-124
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| alphaCoV_Spike_SD1-2_S1-S2_S2 | cd22369 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
600-1262 | 2.01e-118 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) protein from alphacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from alphacoronaviruses including human coronaviruses (HCoVs), HCoV-NL63, and HCoV-229E, and porcine coronaviruses, transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV), among others. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP), and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1 the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411956 [Multi-domain] Cd Length: 666 Bit Score: 383.95 E-value: 2.01e-118
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| HKU1-like_CoV_Spike_S1_RBD | cd21478 | receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1 ... |
294-597 | 3.29e-117 | ||||||||||
receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1 and related coronaviruses; This family contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from human coronavirus (CoV) HKU1, human coronavirus OC43 (HCoV-OC43), mouse hepatitis virus (MHV), porcine hemagglutinating encephalomyelitis virus (HEV), and other related coronaviruses. HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease. HCoV-OC43 is of zoonotic origin and is endemic in the human population, causing mild respiratory tract infections and possible severe complications or fatalities in young children, the elderly, and immunocompromised individuals. MHV is the most common viral pathogen in contemporary laboratory mouse colonies manifesting as a primary infection in the upper respiratory tract. Porcine HEV is associated with acute outbreaks of wasting and encephalitis in nursing piglets from pig farms. These viruses are related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBDs of MHV and HCoV-OC43 are located at the NTD, most CoVs use the C-domain to bind their receptors. Although a protein receptor has not yet been identified for HKU1, antibodies against the C-domain, but not those against the NTD, blocked HKU1 infection of cells, suggesting that the S1 C-domain is the primary HKU1 receptor-binding site. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs. Pssm-ID: 394825 Cd Length: 223 Bit Score: 364.09 E-value: 3.29e-117
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| CoV_Spike_S1_NTD | cd21527 | N-terminal domain of the S1 subunit of coronavirus Spike (S) proteins; This family contains ... |
21-280 | 4.68e-114 | ||||||||||
N-terminal domain of the S1 subunit of coronavirus Spike (S) proteins; This family contains the N-terminal domain (NTD) of the S1 subunit of coronavirus (CoV) Spike (S) proteins from all four (A-D) lineages of betacoronaviruses, including three highly pathogenic human CoVs (HCoV) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as a 2019 novel coronavirus (2019-nCoV) or COVID-19 virus. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). Most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV, use the C-domain to bind their receptors. However, some CoVs from the A lineage, such as mouse hepatitis virus (MHV) uses the NTD to bind its receptor, mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a). Bovine CoV and HCoV-OC43, also from the A lineage, recognize a sugar moiety, 5-N-acetyl-9-O-acetylneuraminic acid (Neu5,9Ac2), on cell-surface glycoproteins or glycolipids; this binding is also through the S1 NTD. The S1 NTD has also been the target for neutralizing antibodies, including human antibody CDC2-A2, and murine antibodies G2 and 5F9, which target MERS-CoV NTD. In addition, the S1 NTD contributes to the Spike trimer interface. Pssm-ID: 394949 Cd Length: 268 Bit Score: 357.56 E-value: 4.68e-114
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| delta-PDCoV-like_Spike_SD1-2_S1-S2_S2 | cd22373 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
604-1262 | 3.35e-113 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from porcine coronavirus HKU15, avian coronaviruses, and related deltacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from porcine coronavirus PDCoV, and several avian coronaviruses such as quail deltacoronavirus (QdCoV) UAE-HKU30, white-eye coronavirus HKU16, common moorhen coronavirus HKU21, thrush CoV HKU12, and munia CoV HKU13, all from the Buldecovirus subgenus of deltacoronaviruses. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411960 [Multi-domain] Cd Length: 648 Bit Score: 369.55 E-value: 3.35e-113
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| HEV_Spike_S1_RBD | cd21508 | receptor-binding domain of the S1 subunit of the Spike (S) protein from porcine ... |
294-594 | 4.36e-110 | ||||||||||
receptor-binding domain of the S1 subunit of the Spike (S) protein from porcine hemagglutinating encephalomyelitis virus; This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from porcine hemagglutinating encephalomyelitis virus (HEV), which is associated with acute outbreaks of wasting and encephalitis in nursing piglets from pig farms. Porcine HEV is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs use the C-domain to bind their receptors. The protein receptor for porcine HEV has not yet been identified. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs. Pssm-ID: 394835 Cd Length: 298 Bit Score: 348.27 E-value: 4.36e-110
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| HCoV-NL63-229E-like_Spike_SD1-2_S1-S2_S2 | cd22375 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
606-1263 | 8.59e-102 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoproteins from HCoV-NL63, HCoV-229E, and related alphacoronavirus; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from alphacoronaviruses, including human coronaviruses (HCoVs), HCoV-NL63 and HCoV-229E. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411962 [Multi-domain] Cd Length: 677 Bit Score: 339.19 E-value: 8.59e-102
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| alphaCoV-HKU2-like_Spike_SD1-2_S1-S2_S2 | cd22371 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the CoV ... |
613-1263 | 1.73e-101 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the CoV spike (S) glycoprotein from Rhinolophus bat coronavirus HKU2 and related alphacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Wencheng shrew coronavirus (WESV), Lucheng Rn rat coronavirus (LRNV), and two bat viruses (Rhinolophus bat coronavirus HKU2 and BtRf-AlphaCoV/YN2012). Members of this group form a distinct cluster that is separated from the other alphacoronaviruses. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411958 [Multi-domain] Cd Length: 686 Bit Score: 338.69 E-value: 1.73e-101
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| TGEV-like_Spike_SD1-2_S1-S2_S2 | cd22377 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
604-1253 | 7.17e-99 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from transmissible gastroenteritis virus and related alphacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from porcine transmissible gastroenteritis virus (TGEV), canine coronavirus (CCoV), and feline coronavirus (FCoV). They display greater than 96% sequence identity and have been grouped in the same species, alphacoronavirus 1, within the Alphacoronavirus genus. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411964 [Multi-domain] Cd Length: 751 Bit Score: 333.27 E-value: 7.17e-99
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| delta-PiCoV-like_Spike_SD1-2_S1-S2_S2 | cd22374 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
599-1263 | 1.74e-98 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Pigeon coronavirus UAE-HKU29, and related avian deltacoronaviruses; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Pigeon coronavirus UAE-HKU29, and related avian deltacoronaviruses including Falcon coronavirus UAE-HKU27, Magpie-robin coronavirus HKU18, Sparrow coronavirus HKU17, and Night heron coronavirus HKU19. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the (C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411961 [Multi-domain] Cd Length: 739 Bit Score: 331.85 E-value: 1.74e-98
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| PDEV-like_Spike_SD1-2_S1-2_S2 | cd22376 | SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) ... |
599-1263 | 1.65e-97 | ||||||||||
SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Porcine epidemic diarrhea virus and related alphacoronavirus; This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from alphacoronaviruses, including porcine epidemic diarrhea virus (PEDV), Scotophilus bat coronavirus, and swine enteric coronavirus, among others. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1 the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. Pssm-ID: 411963 [Multi-domain] Cd Length: 673 Bit Score: 327.10 E-value: 1.65e-97
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| bCoV_S1_N | pfam16451 | Betacoronavirus-like spike glycoprotein S1, N-terminal; This entry represents the N-terminal ... |
28-312 | 2.68e-75 | ||||||||||
Betacoronavirus-like spike glycoprotein S1, N-terminal; This entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like domain (NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Either the S1 NTD or S1 RBD, or occasionally both, are involved in binding to host receptors. S1 NTD is located on the side of the spike trimer and mainly recognizes sugar receptors. For many betacoronaviruses (b-CoVs), for example mouse hepatitis virus (MHV), the RBD is located in the NTD. The structure of the MHV S1 NTD showed the same fold as human galectins (galactose-binding lectin), however it does not bind any sugar; instead, it binds to the carcinoembryonic antigen cell-adhesion molecule CEACAM1) through protein-protein interactions. All three CEACAM21a-binding sites in MHV spikes can be fully occupied by CEACAM1a. It has been shown that CEACAM1a binding to the MHV spike weakens the interactions between S1 and S2 and facilitates the proteolysis of the spike protein and dissociation of S1. The homologous bovine CoV (BCov) S1 NTD also possesses a galectin fold but binds to sialic acid-containing moieties on host cell membranes, as does the NTD of three other group A b-Covs, namely human CoV (HCoV) OC43, avian b-CoV, and infectious bronchitis virus (IBV). Despite the S1 NTD of human respiratory b-CoV HKU1 being highly homologous to the NTDs of MHV and bovine CoV, it does not bind to either sugar or human carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) and the RBD is found instead in the S1 RBD domain. Pssm-ID: 465119 Cd Length: 296 Bit Score: 251.95 E-value: 2.68e-75
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| CoV_Spike_S1_RBD | cd21470 | receptor-binding domain of the S1 subunit of coronavirus spike (S) proteins; This family ... |
298-461 | 4.69e-63 | ||||||||||
receptor-binding domain of the S1 subunit of coronavirus spike (S) proteins; This family contains the receptor-binding domain (RBD) of the S1 subunit of coronavirus (CoV) spike (S) proteins from three highly pathogenic human coronaviruses (CoVs), including Middle East respiratory syndrome coronavirus (MERS-CoV), Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS coronavirus 2 (SARS-CoV-2), also known as a 2019 novel coronavirus (2019-nCoV), as well as S proteins from related coronaviruses. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. MHV uses mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a) as the receptor, and the receptors for SARS-CoV and MERS-CoV are human angiotensin-converting enzyme 2 (ACE2) and human dipeptidyl peptidase 4 (DPP4), respectively. Recent studies found that the RBD of SARS-CoV-2 S protein binds strongly to human and bat angiotensin-converting enzyme 2 (ACE2) receptors. Moreover, SARS-CoV-2 RBD exhibited significantly higher binding affinity to the ACE2 receptor than SARS-CoV RBD. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs. Pssm-ID: 394823 Cd Length: 171 Bit Score: 211.96 E-value: 4.69e-63
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| bCoV_S1_RBD | pfam09408 | Betacoronavirus spike glycoprotein S1, receptor binding; This entry represents the receptor ... |
326-483 | 1.22e-30 | ||||||||||
Betacoronavirus spike glycoprotein S1, receptor binding; This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilize both the S1 NTD and S1 RBD for viral entry. SARS-CoV makes use of its S1 RBD to bind to the human angiotensin-converting enzyme 2 (ACE2) as its host receptor. Pssm-ID: 462789 Cd Length: 156 Bit Score: 118.76 E-value: 1.22e-30
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| MERS-like_CoV_Spike_S1_RBD | cd21479 | receptor-binding domain of the S1 subunit of the Spike (S) protein from Middle East ... |
298-448 | 9.95e-24 | ||||||||||
receptor-binding domain of the S1 subunit of the Spike (S) protein from Middle East respiratory syndrome coronavirus; This family contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from the human coronavirus that causes Middle East Respiratory Syndrome (MERS-CoV) and related coronaviruses from animals. MERS-CoV causes severe pulmonary disease in humans. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including MERS-CoV use the C-domain to bind their receptors. MERS-CoV use human dipeptidyl peptidase 4 (DPP4), also called CD26, as its receptor. It binds DPP4 through the RBD of its S1 subunit and then fuses viral and host membranes through its S2 subunit. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs including MERS-CoV. Pssm-ID: 394826 Cd Length: 216 Bit Score: 100.93 E-value: 9.95e-24
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| bat_HKU4-like_Spike_S1_RBD | cd21487 | receptor-binding domain of the S1 subunit of the Spike (S) protein from Tylonycteris bat ... |
309-431 | 6.46e-21 | ||||||||||
receptor-binding domain of the S1 subunit of the Spike (S) protein from Tylonycteris bat coronavirus HKU4 and similar proteins; This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from Tylonycteris bat coronavirus HKU4 and other Middle East Respiratory Syndrome (MERS)-related coronaviruses. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including human MERS-CoV that is phylogenetically closely related to bat CoV HKU4 use the C-domain to bind their receptors. HKU4 is able to bind the MERS-CoV receptor, human dipeptidyl peptidase 4 (DPP4), also called CD26. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs including MERS-CoV, and most likely, bat CoV HKU4. Pssm-ID: 394834 Cd Length: 219 Bit Score: 92.73 E-value: 6.46e-21
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| human_MERS-CoV_Spike_S1_RBD | cd21486 | receptor-binding domain of the S1 subunit of the Spike (S) protein from human Middle East ... |
299-417 | 7.60e-15 | ||||||||||
receptor-binding domain of the S1 subunit of the Spike (S) protein from human Middle East respiratory syndrome coronavirus; This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from the human coronavirus that causes Middle East Respiratory Syndrome (MERS-CoV). MERS-CoV causes severe pulmonary disease in humans. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including MERS-CoV use the C-domain to bind their receptors. MERS-CoV use human dipeptidyl peptidase 4 (DPP4), also called CD26, as its receptor. It binds DPP4 through the RBD of its S1 subunit and then fuses viral and host membranes through its S2 subunit. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs including MERS-CoV. Pssm-ID: 394833 Cd Length: 219 Bit Score: 75.17 E-value: 7.60e-15
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| SARS-CoV-like_Spike_S1_NTD | cd21624 | N-terminal domain of the S1 subunit of the Spike (S) protein from Severe acute respiratory ... |
34-281 | 4.89e-12 | ||||||||||
N-terminal domain of the S1 subunit of the Spike (S) protein from Severe acute respiratory syndrome coronavirus and related betacoronaviruses in the B lineage; This subfamily contains the N-terminal domain (NTD) of the S1 subunit of the Spike (S) proteins from betacoronaviruses in the sarbecovirus subgenera (B lineage), including the highly pathogenic human coronavirus (CoV), Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as a 2019 novel coronavirus (2019-nCoV) or COVID-19 virus. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). Most CoVs, including SARS-CoV-2 and SARS-CoV, use the C-domain to bind their receptors. The S1 NTD contributes to the Spike trimer interface. Pssm-ID: 394950 Cd Length: 280 Bit Score: 68.13 E-value: 4.89e-12
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| CoV_S1_C | pfam19209 | Coronavirus spike glycoprotein S1, C-terminal; This entry represents a domain found at the ... |
604-661 | 6.13e-12 | ||||||||||
Coronavirus spike glycoprotein S1, C-terminal; This entry represents a domain found at the C-terminus of the Coronavirus S1 protein. It is found across a range of alpha, beta and gamma coronaviruses. This small all beta stranded domain is known as subdomain 2 in the structure of the porcine epidemic diarrhea virus spike protein. Pssm-ID: 437047 [Multi-domain] Cd Length: 57 Bit Score: 61.87 E-value: 6.13e-12
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| Fibritin_C | pfam07921 | Fibritin C-terminal region; This family features sequences bearing similarity to the ... |
1258-1291 | 3.40e-08 | ||||||||||
Fibritin C-terminal region; This family features sequences bearing similarity to the C-terminal portion of the bacteriophage T4 protein fibritin. This protein is responsible for attachment of long tail fibres to virus particle, and forms the 'whiskers' or fibres on the neck of the virion. The region seen in this family contains an N-terminal coiled-coil portion and the C-terminal globular foldon domain (residues 457-486), which is essential for fibritin trimerization and folding. This domain consists of a beta-hairpin; three such hairpins come together in a beta-propeller-like arrangement in the trimer, which is stabilized by hydrogen bonds, salt bridges and hydrophobic interactions. Pssm-ID: 254516 [Multi-domain] Cd Length: 93 Bit Score: 52.46 E-value: 3.40e-08
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| MERS-CoV-like_Spike_S1_NTD | cd21626 | N-terminal domain of the S1 subunit of the Spike (S) protein from Middle East respiratory ... |
27-279 | 3.40e-08 | ||||||||||
N-terminal domain of the S1 subunit of the Spike (S) protein from Middle East respiratory syndrome-related coronavirus and related betacoronaviruses in the C lineage; This subfamily contains the N-terminal domain (NTD) of the S1 subunit of the Spike (S) proteins from betacoronaviruses in the merbecovirus subgenera (C lineage), including the highly pathogenic human coronavirus (CoV), Middle East respiratory syndrome (MERS)-related CoV, and related bat CoVs. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). Most CoVs, including MERS-CoV, use the C-domain to bind their receptors. Despite using the C-domain as its receptor, neutralizing antibodies targeting MERS-CoV S1-NTD have been reported, including human antibody CDC2-A2, murine antibodies G2 and 5F9, and macaque antibodies FIB-H1 and JC57-13. G2 has been shown to strongly disrupt the attachment of MERS-CoV S to its receptor, dipeptidyl peptidase-4 (DPP4). In addition, the S1 NTD contributes to the Spike trimer interface. Pssm-ID: 394952 Cd Length: 328 Bit Score: 56.97 E-value: 3.40e-08
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| SARS-CoV_Spike_S1_RBD | cd21481 | receptor-binding domain of the S1 subunit of severe acute respiratory syndrome-related ... |
307-467 | 1.63e-07 | ||||||||||
receptor-binding domain of the S1 subunit of severe acute respiratory syndrome-related coronavirus Spike (S) protein; This group contains the receptor-binding domain of the S1 subunit of the spike (S) protein from severe acute respiratory syndrome-related coronavirus (SARS-CoV) and similar coronaviruses. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV use the C-domain to bind their receptors. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for SARS-CoV and most CoVs. Pssm-ID: 394828 Cd Length: 222 Bit Score: 53.54 E-value: 1.63e-07
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| wac | PHA02607 | fibritin; Provisional |
1255-1292 | 1.72e-06 | ||||||||||
fibritin; Provisional Pssm-ID: 177432 [Multi-domain] Cd Length: 454 Bit Score: 51.95 E-value: 1.72e-06
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| SARS-CoV-2_Spike_S1_RBD | cd21480 | receptor-binding domain of the S1 subunit of severe acute respiratory syndrome coronavirus 2 ... |
298-415 | 8.21e-06 | ||||||||||
receptor-binding domain of the S1 subunit of severe acute respiratory syndrome coronavirus 2 Spike (S) protein; This group contains the receptor-binding domain of the S1 subunit of the spike (S) protein from highly pathogenic human virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as 2019 novel coronavirus (2019-nCoV). The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While RBD of mouse hepatitis virus (MHV) is located at the NTD, most of other CoVs, including SARS-CoV-2 use the C-domain to bind their receptors. Recent studies found that the receptor-binding domain (RBD) of SARS-CoV-2 S protein binds strongly to human and bat angiotensin-converting enzyme 2 (ACE2) receptors. Moreover, SARS-CoV-2 RBD exhibited significantly higher binding affinity to the ACE2 receptor than SARS-CoV RBD. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for SARS-CoV-2 and most CoVs. Pssm-ID: 394827 Cd Length: 223 Bit Score: 48.55 E-value: 8.21e-06
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| SARS-CoV-like_Spike_S1_RBD | cd21477 | receptor-binding domain of the S1 subunit of severe acute respiratory syndrome-related ... |
298-403 | 1.91e-05 | ||||||||||
receptor-binding domain of the S1 subunit of severe acute respiratory syndrome-related coronavirus Spike (S) protein and similar proteins; This subfamily contains the receptor-binding domain of the S1 subunit of coronavirus (CoV) spike (S) proteins from highly pathogenic human virus, severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), SARS coronavirus 2 (SARS-CoV-2), also known as 2019 novel coronavirus (2019-nCoV), and other SARS-like coronaviruses. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2 and SARS-CoV use the C-domain to bind their receptors. Recent studies found that the receptor-binding domain (RBD) of SARS-CoV-2 S protein binds strongly to human and bat angiotensin-converting enzyme 2 (ACE2) receptors. Moreover, SARS-CoV-2 RBD exhibited significantly higher binding affinity to the ACE2 receptor than SARS-CoV RBD. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for SARS-CoV, SARS-CoV-2, and most CoVs. Pssm-ID: 394824 Cd Length: 205 Bit Score: 47.12 E-value: 1.91e-05
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| batCoV-HKU9-like_Spike_S1_NTD | cd21627 | N-terminal domain of the S1 subunit of the Spike (S) protein from Rousettus bat coronavirus ... |
170-279 | 8.72e-03 | ||||||||||
N-terminal domain of the S1 subunit of the Spike (S) protein from Rousettus bat coronavirus HKU9 and related betacoronaviruses in the D lineage; This subfamily contains the N-terminal domain (NTD) of the S1 subunit of the Spike (S) proteins from betacoronaviruses in the nobecovirus subgenera (D lineage), including Rousettus bat coronavirus HKU9 and related bat CoVs. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). Most CoVs, including SARS-CoV-2, SARS-CoV, and MERS-CoV use the C-domain to bind their receptors. However, CoV such as mouse hepatitis virus (MHV) uses the NTD to bind its receptor, mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a). The S1 NTD contributes to the Spike trimer interface. Pssm-ID: 394953 Cd Length: 289 Bit Score: 39.64 E-value: 8.72e-03
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