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Conserved domains on  [gi|1967465497|gb|QQY96591|]
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N [Transmissible gastroenteritis virus]

Protein Classification

nucleocapsid protein( domain architecture ID 10469632)

nucleocapsid (N) protein packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M

Gene Ontology:  GO:0019013

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CoV_nucleocap pfam00937
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 23-359 3.50e-133

Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved domains. The N-terminal domain (NTD) (N1b), the C-terminal domain (CTD)(N2b) and the N3 region. The N1b and N2b domains from SARS CoV, infectious bronchitis virus (IBV), human CoV 229E and mouse hepatic virus (MHV) display similar topological organizations. N proteins form dimers, which are asymmetrically arranged into octamers via their N2b domains. Domains N1b and N2b are linked by another domain N2a that contains an SR-rich region in which phosphorylation of specific serine residues allows the N protein to associate with the RNA helicase DDX1 permitting template read-through, and enabling the transition from discontinuous transcription of subgenomic mRNAs (sgmRNAs) to continuous synthesis of longer sgmRNAs and genomic RNA (gRNA). It has been shown that N proteins interact with nonstructural protein 3 (NSP3) and thus are recruited to the replication-transcription complexes (RTCs).


:

Pssm-ID: 460005 [Multi-domain]  Cd Length: 343  Bit Score: 384.78  E-value: 3.50e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497  23 SRGRKNNNIPLSFFNPITLQQGSKFWNLCPRDFVPKGIGNRDQQIGYWNRQTRYRMVKGQRKELPERWFFYYLGTGPHAD 102
Cdd:pfam00937   1 MAPRRNGRVPLSWFQPITQQGKKNFWKVMPGNGVPKGKGNKDQQIGYWNRQPRYRMGKGQRKQLPPRWYFYYLGTGPHAN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497 103 AKFKDKLDGVVWVAKDGAMNKPT-TLGSRGANNESKALKFDGKVPGEFQLEVNQSRDNSRSRSQ-----SRSRSRNRSQS 176
Cdd:pfam00937  81 LKFGERIDGVFWVAKDGAKTSPTgKLGTRNPNHEALPLRFPPGLPKGFEIEGNGRSRPNSRSQSrsrsrARSRSGSNSRS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497 177 RGRQQFNNKKDDSVEQAVLAALKKLGVDTEKQQqrSRSKSKERSNSKTRDTTPKNENKHTWKRTAGKG-DVTRFYGARSS 255
Cdd:pfam00937 161 QSRGRSGSNGQDDLVAAVLQALKELGVKKEGKK--GKSTPKKRTKSAAARTKPKQLNKPRWKRTPNKGeNVTQCFGPRSP 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497 256 SANFGDTDLVANGSSAKHYPQLAECVPSVSSILFGSYWTSKEDGDQIEVTFTHKYHLPKDDPKTGQFLQQINAYARPSEV 335
Cdd:pfam00937 239 GKNFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKEQGDDVELTYTYKIKVPKDNPNLERFLEQLNAYVDPYKE 318

                         330       340
                  ....*....|....*....|....*
gi 1967465497 336 AKEQRKRKSRSKS-AERSEQDVVPD 359
Cdd:pfam00937 319 FPPKPQKKKKKQSkLKPQAPAFTPK 343
 
Name Accession Description Interval E-value
CoV_nucleocap pfam00937
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 23-359 3.50e-133

Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved domains. The N-terminal domain (NTD) (N1b), the C-terminal domain (CTD)(N2b) and the N3 region. The N1b and N2b domains from SARS CoV, infectious bronchitis virus (IBV), human CoV 229E and mouse hepatic virus (MHV) display similar topological organizations. N proteins form dimers, which are asymmetrically arranged into octamers via their N2b domains. Domains N1b and N2b are linked by another domain N2a that contains an SR-rich region in which phosphorylation of specific serine residues allows the N protein to associate with the RNA helicase DDX1 permitting template read-through, and enabling the transition from discontinuous transcription of subgenomic mRNAs (sgmRNAs) to continuous synthesis of longer sgmRNAs and genomic RNA (gRNA). It has been shown that N proteins interact with nonstructural protein 3 (NSP3) and thus are recruited to the replication-transcription complexes (RTCs).


Pssm-ID: 460005 [Multi-domain]  Cd Length: 343  Bit Score: 384.78  E-value: 3.50e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497  23 SRGRKNNNIPLSFFNPITLQQGSKFWNLCPRDFVPKGIGNRDQQIGYWNRQTRYRMVKGQRKELPERWFFYYLGTGPHAD 102
Cdd:pfam00937   1 MAPRRNGRVPLSWFQPITQQGKKNFWKVMPGNGVPKGKGNKDQQIGYWNRQPRYRMGKGQRKQLPPRWYFYYLGTGPHAN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497 103 AKFKDKLDGVVWVAKDGAMNKPT-TLGSRGANNESKALKFDGKVPGEFQLEVNQSRDNSRSRSQ-----SRSRSRNRSQS 176
Cdd:pfam00937  81 LKFGERIDGVFWVAKDGAKTSPTgKLGTRNPNHEALPLRFPPGLPKGFEIEGNGRSRPNSRSQSrsrsrARSRSGSNSRS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497 177 RGRQQFNNKKDDSVEQAVLAALKKLGVDTEKQQqrSRSKSKERSNSKTRDTTPKNENKHTWKRTAGKG-DVTRFYGARSS 255
Cdd:pfam00937 161 QSRGRSGSNGQDDLVAAVLQALKELGVKKEGKK--GKSTPKKRTKSAAARTKPKQLNKPRWKRTPNKGeNVTQCFGPRSP 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497 256 SANFGDTDLVANGSSAKHYPQLAECVPSVSSILFGSYWTSKEDGDQIEVTFTHKYHLPKDDPKTGQFLQQINAYARPSEV 335
Cdd:pfam00937 239 GKNFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKEQGDDVELTYTYKIKVPKDNPNLERFLEQLNAYVDPYKE 318

                         330       340
                  ....*....|....*....|....*
gi 1967465497 336 AKEQRKRKSRSKS-AERSEQDVVPD 359
Cdd:pfam00937 319 FPPKPQKKKKKQSkLKPQAPAFTPK 343
CoV_N-NTD cd21554
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 31-151 6.74e-58

N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) protein is a major structural and multifunctional protein. It plays an important role in the virus replication cycle, by forming a complex with the viral RNA through its N-terminal domain (N-NTD), which makes this domain an important drug target. It also interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly.


Pssm-ID: 439219  Cd Length: 123  Bit Score: 184.33  E-value: 6.74e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497  31 IPLSFFNPITLQQGSK-FWNLcPRDFVPKGIGNRDQQIGYWNRQTRYRMVKGQRKELPERWFFYYLGTGPHADAKFKDKL 109
Cdd:cd21554     1 IPLSWFAPITQTGKNKpFFKV-PQGVPPNGGGPKDQQIGYWNRQPRWRMGKGGRKPLPPRWYFYYLGTGPHADLKYGERI 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1967465497 110 DGVVWVAKDGAM-NKPTTLGSRGANN-ESKALKFDGKVPGEFQL 151
Cdd:cd21554    80 DGVVWVAKEGADtNTPTDLGTRNPNNdEAIPLRFPPGLPKGFYI 123
 
Name Accession Description Interval E-value
CoV_nucleocap pfam00937
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 23-359 3.50e-133

Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved domains. The N-terminal domain (NTD) (N1b), the C-terminal domain (CTD)(N2b) and the N3 region. The N1b and N2b domains from SARS CoV, infectious bronchitis virus (IBV), human CoV 229E and mouse hepatic virus (MHV) display similar topological organizations. N proteins form dimers, which are asymmetrically arranged into octamers via their N2b domains. Domains N1b and N2b are linked by another domain N2a that contains an SR-rich region in which phosphorylation of specific serine residues allows the N protein to associate with the RNA helicase DDX1 permitting template read-through, and enabling the transition from discontinuous transcription of subgenomic mRNAs (sgmRNAs) to continuous synthesis of longer sgmRNAs and genomic RNA (gRNA). It has been shown that N proteins interact with nonstructural protein 3 (NSP3) and thus are recruited to the replication-transcription complexes (RTCs).


Pssm-ID: 460005 [Multi-domain]  Cd Length: 343  Bit Score: 384.78  E-value: 3.50e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497  23 SRGRKNNNIPLSFFNPITLQQGSKFWNLCPRDFVPKGIGNRDQQIGYWNRQTRYRMVKGQRKELPERWFFYYLGTGPHAD 102
Cdd:pfam00937   1 MAPRRNGRVPLSWFQPITQQGKKNFWKVMPGNGVPKGKGNKDQQIGYWNRQPRYRMGKGQRKQLPPRWYFYYLGTGPHAN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497 103 AKFKDKLDGVVWVAKDGAMNKPT-TLGSRGANNESKALKFDGKVPGEFQLEVNQSRDNSRSRSQ-----SRSRSRNRSQS 176
Cdd:pfam00937  81 LKFGERIDGVFWVAKDGAKTSPTgKLGTRNPNHEALPLRFPPGLPKGFEIEGNGRSRPNSRSQSrsrsrARSRSGSNSRS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497 177 RGRQQFNNKKDDSVEQAVLAALKKLGVDTEKQQqrSRSKSKERSNSKTRDTTPKNENKHTWKRTAGKG-DVTRFYGARSS 255
Cdd:pfam00937 161 QSRGRSGSNGQDDLVAAVLQALKELGVKKEGKK--GKSTPKKRTKSAAARTKPKQLNKPRWKRTPNKGeNVTQCFGPRSP 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497 256 SANFGDTDLVANGSSAKHYPQLAECVPSVSSILFGSYWTSKEDGDQIEVTFTHKYHLPKDDPKTGQFLQQINAYARPSEV 335
Cdd:pfam00937 239 GKNFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKEQGDDVELTYTYKIKVPKDNPNLERFLEQLNAYVDPYKE 318

                         330       340
                  ....*....|....*....|....*
gi 1967465497 336 AKEQRKRKSRSKS-AERSEQDVVPD 359
Cdd:pfam00937 319 FPPKPQKKKKKQSkLKPQAPAFTPK 343
CoV_N-NTD cd21554
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 31-151 6.74e-58

N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) protein is a major structural and multifunctional protein. It plays an important role in the virus replication cycle, by forming a complex with the viral RNA through its N-terminal domain (N-NTD), which makes this domain an important drug target. It also interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly.


Pssm-ID: 439219  Cd Length: 123  Bit Score: 184.33  E-value: 6.74e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497  31 IPLSFFNPITLQQGSK-FWNLcPRDFVPKGIGNRDQQIGYWNRQTRYRMVKGQRKELPERWFFYYLGTGPHADAKFKDKL 109
Cdd:cd21554     1 IPLSWFAPITQTGKNKpFFKV-PQGVPPNGGGPKDQQIGYWNRQPRWRMGKGGRKPLPPRWYFYYLGTGPHADLKYGERI 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1967465497 110 DGVVWVAKDGAM-NKPTTLGSRGANN-ESKALKFDGKVPGEFQL 151
Cdd:cd21554    80 DGVVWVAKEGADtNTPTDLGTRNPNNdEAIPLRFPPGLPKGFYI 123
CoV_N-CTD cd21595
C-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 245-328 9.12e-38

C-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) protein is a major structural and multifunctional protein. It plays an important role in the virus replication cycle, by forming a complex with the viral RNA. It also interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly. The C-terminal domain of the N protein (N-CTD) is involved in dimerization, and is thus, also called the dimerization domain.


Pssm-ID: 439220  Cd Length: 84  Bit Score: 130.68  E-value: 9.12e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1967465497 245 DVTRFYGARSSSANFGDTDLVANGSSAKHYPQLAECVPSVSSILFGSYWTSKEDGDQIEVTFTHKYHLPKDDPKTGQFLQ 324
Cdd:cd21595     1 NVTQCFGPRGPEGNFGDADLVKLGVDDPRFPQLAELVPSPAALLFGSHVSTKEQGDGVELTYTYKIKVPKDDKNLKAFLE 80


                  ....
gi 1967465497 325 QINA 328
Cdd:cd21595    81 QVDA 84
 
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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