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Conserved domains on  [gi|54310714|ref|YP_133826|]
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fusion protein [peste-des-petits-ruminants virus]

Protein Classification

fusion glycoprotein F0( domain architecture ID 10455199)

fusion glycoprotein F0 is a class I viral fusion protein that directs fusion of viral and cellular membranes, resulting in viral penetration, and can direct fusion of infected cells with adjoining cells, resulting in the formation of syncytia.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Fusion_gly pfam00523
Fusion glycoprotein F0;
22-483 0e+00

Fusion glycoprotein F0;


:

Pssm-ID: 395418  Cd Length: 473  Bit Score: 561.24  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714    22 HWGNLSKIGIVGTGSASYKVMTRPSHQTLVIKLMPNITAIDNCTKSEIAEYKRLLITVLKPVEDALSVITKNVRPIQTLT 101
Cdd:pfam00523   1 DEDNLSKIGVVVTGGKFLKIRTSSSTSYIVIKLLPNIGNTNKCTKTEVDQYKNTLTTLLTPIADALNRIEAPITVLTSTI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714   102 PGRRTRRFAGAVLAGVALGVATAAQITAGVALHQSLMNSQAIESLKTSLEKSNQAIEEIRLANKETILAVQGVQDYINNE 181
Cdd:pfam00523  81 SSKRKKRFAGAVIGGIALGVATAAQITAGIALAQALENAGAIAKIKNSIQATNEAVVKLQNGVSVLATAVNALQDFINTQ 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714   182 LVPSVHRMSCELVGHKLGLKLLRYYTEILSIFGPSLRDPIAAEISIQALSYALGGDINRILDKLGYSGGDFLAILESKGI 261
Cdd:pfam00523 161 LNPAINQLSCDIADLKLGISLTQYLSELLTVFGPNLGNPVENPLSIQALSSLLGGNLNALVTKLGYTNSDILDLLSSRSI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714   262 KARVTYVDTRDYFIILSIAYPTLSEIKGVIVHKIEAITYNIGAQEWYTTIPKYVATQGYLISNFDETSCVFTPDGTVCSQ 341
Cdd:pfam00523 241 KGQIILVDLEEYMIVLSVQLPILGEIDNTLVKELSSISYNIDGQEWYTQVPKVVLNRGSLISGPDASDCKVTSLHVICDQ 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714   342 NALYPMSPLLQECFQGSTKSCARTLVSGTISNRFILSKGNLIANCASVLCKCYTTETVISQDPDKLLTVVASDKCPVVEV 421
Cdd:pfam00523 321 DPAFPMSPEVQECLSGNTYACPRSTVVGSISPRFATSLGAIVANCISTTCLCGTPGRPIIQPGSKGLTYISNDDCDTVSV 400

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54310714   422 DGVTIQVGSREYPDSVYLHKIDLGPAISLEKLDVGTNLGNAVTRLENAKELLDASDQILKTV 483
Cdd:pfam00523 401 DGIVIYLSKKFDNVTGNNLTIKLGPPINTPPLDISTELSKVNESLQQSKDLLEESNKILDSV 462
 
Name Accession Description Interval E-value
Fusion_gly pfam00523
Fusion glycoprotein F0;
22-483 0e+00

Fusion glycoprotein F0;


Pssm-ID: 395418  Cd Length: 473  Bit Score: 561.24  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714    22 HWGNLSKIGIVGTGSASYKVMTRPSHQTLVIKLMPNITAIDNCTKSEIAEYKRLLITVLKPVEDALSVITKNVRPIQTLT 101
Cdd:pfam00523   1 DEDNLSKIGVVVTGGKFLKIRTSSSTSYIVIKLLPNIGNTNKCTKTEVDQYKNTLTTLLTPIADALNRIEAPITVLTSTI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714   102 PGRRTRRFAGAVLAGVALGVATAAQITAGVALHQSLMNSQAIESLKTSLEKSNQAIEEIRLANKETILAVQGVQDYINNE 181
Cdd:pfam00523  81 SSKRKKRFAGAVIGGIALGVATAAQITAGIALAQALENAGAIAKIKNSIQATNEAVVKLQNGVSVLATAVNALQDFINTQ 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714   182 LVPSVHRMSCELVGHKLGLKLLRYYTEILSIFGPSLRDPIAAEISIQALSYALGGDINRILDKLGYSGGDFLAILESKGI 261
Cdd:pfam00523 161 LNPAINQLSCDIADLKLGISLTQYLSELLTVFGPNLGNPVENPLSIQALSSLLGGNLNALVTKLGYTNSDILDLLSSRSI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714   262 KARVTYVDTRDYFIILSIAYPTLSEIKGVIVHKIEAITYNIGAQEWYTTIPKYVATQGYLISNFDETSCVFTPDGTVCSQ 341
Cdd:pfam00523 241 KGQIILVDLEEYMIVLSVQLPILGEIDNTLVKELSSISYNIDGQEWYTQVPKVVLNRGSLISGPDASDCKVTSLHVICDQ 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714   342 NALYPMSPLLQECFQGSTKSCARTLVSGTISNRFILSKGNLIANCASVLCKCYTTETVISQDPDKLLTVVASDKCPVVEV 421
Cdd:pfam00523 321 DPAFPMSPEVQECLSGNTYACPRSTVVGSISPRFATSLGAIVANCISTTCLCGTPGRPIIQPGSKGLTYISNDDCDTVSV 400

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54310714   422 DGVTIQVGSREYPDSVYLHKIDLGPAISLEKLDVGTNLGNAVTRLENAKELLDASDQILKTV 483
Cdd:pfam00523 401 DGIVIYLSKKFDNVTGNNLTIKLGPPINTPPLDISTELSKVNESLQQSKDLLEESNKILDSV 462
PHA03332 PHA03332
membrane glycoprotein; Provisional
 104-178 1.48e-03

membrane glycoprotein; Provisional


Pssm-ID: 223047 [Multi-domain]  Cd Length: 1328  Bit Score: 41.49  E-value: 1.48e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54310714   104 RRTRRFAGAVLAGVALGVATAAQITAGVALHQSLMNSQAIESLKTSLEKSNQAIEEIRLANKETILAVQGVQDYI 178
Cdd:PHA03332  840 FAPRRFGGSVMAGDAIGLSAAAFTMASAALNAATQALAVATLYVNQLLQATAATAEMASKIGGLNARVDKTSDVI 914
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) ...
 55-179 2.58e-03

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: 40.74  E-value: 2.58e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714  55 MPNITAIDNCTKSEIAEYKRLL-------ITVLKPVEDAlsvitknvrPIQTLtpgrrtrrFAGAVLAGVALGVATAA-- 125
Cdd:cd22372 284 LPTDDAYKKCTAGPLGFLKDLVcaqeyngLLVLPPIITA---------EMQTM--------YTGSLVASMAFGGITAAga 346

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54310714 126 -----QITAGV---ALHQS-LMNSQaiESLKTSLeksNQAIEEIRLANKETILAVQGVQDYIN 179
Cdd:cd22372 347 ipfatQIQARInhlGITQSlLLKNQ--EKIAASF---NKAIGHMQEGFRSTSLALQQIQDVVN 404
 
Name Accession Description Interval E-value
Fusion_gly pfam00523
Fusion glycoprotein F0;
22-483 0e+00

Fusion glycoprotein F0;


Pssm-ID: 395418  Cd Length: 473  Bit Score: 561.24  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714    22 HWGNLSKIGIVGTGSASYKVMTRPSHQTLVIKLMPNITAIDNCTKSEIAEYKRLLITVLKPVEDALSVITKNVRPIQTLT 101
Cdd:pfam00523   1 DEDNLSKIGVVVTGGKFLKIRTSSSTSYIVIKLLPNIGNTNKCTKTEVDQYKNTLTTLLTPIADALNRIEAPITVLTSTI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714   102 PGRRTRRFAGAVLAGVALGVATAAQITAGVALHQSLMNSQAIESLKTSLEKSNQAIEEIRLANKETILAVQGVQDYINNE 181
Cdd:pfam00523  81 SSKRKKRFAGAVIGGIALGVATAAQITAGIALAQALENAGAIAKIKNSIQATNEAVVKLQNGVSVLATAVNALQDFINTQ 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714   182 LVPSVHRMSCELVGHKLGLKLLRYYTEILSIFGPSLRDPIAAEISIQALSYALGGDINRILDKLGYSGGDFLAILESKGI 261
Cdd:pfam00523 161 LNPAINQLSCDIADLKLGISLTQYLSELLTVFGPNLGNPVENPLSIQALSSLLGGNLNALVTKLGYTNSDILDLLSSRSI 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714   262 KARVTYVDTRDYFIILSIAYPTLSEIKGVIVHKIEAITYNIGAQEWYTTIPKYVATQGYLISNFDETSCVFTPDGTVCSQ 341
Cdd:pfam00523 241 KGQIILVDLEEYMIVLSVQLPILGEIDNTLVKELSSISYNIDGQEWYTQVPKVVLNRGSLISGPDASDCKVTSLHVICDQ 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714   342 NALYPMSPLLQECFQGSTKSCARTLVSGTISNRFILSKGNLIANCASVLCKCYTTETVISQDPDKLLTVVASDKCPVVEV 421
Cdd:pfam00523 321 DPAFPMSPEVQECLSGNTYACPRSTVVGSISPRFATSLGAIVANCISTTCLCGTPGRPIIQPGSKGLTYISNDDCDTVSV 400

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 54310714   422 DGVTIQVGSREYPDSVYLHKIDLGPAISLEKLDVGTNLGNAVTRLENAKELLDASDQILKTV 483
Cdd:pfam00523 401 DGIVIYLSKKFDNVTGNNLTIKLGPPINTPPLDISTELSKVNESLQQSKDLLEESNKILDSV 462
PHA03332 PHA03332
membrane glycoprotein; Provisional
 104-178 1.48e-03

membrane glycoprotein; Provisional


Pssm-ID: 223047 [Multi-domain]  Cd Length: 1328  Bit Score: 41.49  E-value: 1.48e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 54310714   104 RRTRRFAGAVLAGVALGVATAAQITAGVALHQSLMNSQAIESLKTSLEKSNQAIEEIRLANKETILAVQGVQDYI 178
Cdd:PHA03332  840 FAPRRFGGSVMAGDAIGLSAAAFTMASAALNAATQALAVATLYVNQLLQATAATAEMASKIGGLNARVDKTSDVI 914
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) ...
 55-179 2.58e-03

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: 40.74  E-value: 2.58e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 54310714  55 MPNITAIDNCTKSEIAEYKRLL-------ITVLKPVEDAlsvitknvrPIQTLtpgrrtrrFAGAVLAGVALGVATAA-- 125
Cdd:cd22372 284 LPTDDAYKKCTAGPLGFLKDLVcaqeyngLLVLPPIITA---------EMQTM--------YTGSLVASMAFGGITAAga 346

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 54310714 126 -----QITAGV---ALHQS-LMNSQaiESLKTSLeksNQAIEEIRLANKETILAVQGVQDYIN 179
Cdd:cd22372 347 ipfatQIQARInhlGITQSlLLKNQ--EKIAASF---NKAIGHMQEGFRSTSLALQQIQDVVN 404
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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