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Conserved domains on  [gi|1798174255|ref|YP_009724397|]
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nucleocapsid phosphoprotein [Severe acute respiratory syndrome coronavirus 2]

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 super family cl47612
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 46-388 2.18e-87

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).


The actual alignment was detected with superfamily member pfam00937:

Pssm-ID: 460005 [Multi-domain]  Cd Length: 343  Bit Score: 269.22  E-value: 2.18e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255  46 PNNTASWFTALTQHG-KEDLKFPRGQGVPINTNSsPDDQIGYYRRATRrIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYG 124
Cdd:pfam00937   7 GRVPLSWFQPITQQGkKNFWKVMPGNGVPKGKGN-KDQQIGYWNRQPR-YRMGKGQRKQLPPRWYFYYLGTGPHANLKFG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255 125 ANKDGIIWVATEGALNTPKDHIGTRNPaNNAAIVLQLPQGttLPKGFYAEGSrGGSQASSRSSSRSRNSSRNSTPGSSRG 204
Cdd:pfam00937  85 ERIDGVFWVAKDGAKTSPTGKLGTRNP-NHEALPLRFPPG--LPKGFEIEGN-GRSRPNSRSQSRSRSRARSRSGSNSRS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255 205 TSPARmAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASK----KPRQKRTATKAYNVTQAFGRRGPE 280
Cdd:pfam00937 161 QSRGR-SGSNGQDDLVAAVLQALKELGVKKEGKKGKSTPKKRTKSAAARTKPkqlnKPRWKRTPNKGENVTQCFGPRSPG 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255 281 QtqgNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAY 360
Cdd:pfam00937 240 K---NFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKEQGDDVELTYTYKIKVPKDNPNLERFLEQLNAYVDPY 316

                         330       340
                  ....*....|....*....|....*...
gi 1798174255 361 KTFPPTEPKKDKKKKADETQAlPQRQKK 388
Cdd:pfam00937 317 KEFPPKPQKKKKKQSKLKPQA-PAFTPK 343
 
Name Accession Description Interval E-value
CoV_nucleocap pfam00937
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 46-388 2.18e-87

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: 269.22  E-value: 2.18e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255  46 PNNTASWFTALTQHG-KEDLKFPRGQGVPINTNSsPDDQIGYYRRATRrIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYG 124
Cdd:pfam00937   7 GRVPLSWFQPITQQGkKNFWKVMPGNGVPKGKGN-KDQQIGYWNRQPR-YRMGKGQRKQLPPRWYFYYLGTGPHANLKFG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255 125 ANKDGIIWVATEGALNTPKDHIGTRNPaNNAAIVLQLPQGttLPKGFYAEGSrGGSQASSRSSSRSRNSSRNSTPGSSRG 204
Cdd:pfam00937  85 ERIDGVFWVAKDGAKTSPTGKLGTRNP-NHEALPLRFPPG--LPKGFEIEGN-GRSRPNSRSQSRSRSRARSRSGSNSRS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255 205 TSPARmAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASK----KPRQKRTATKAYNVTQAFGRRGPE 280
Cdd:pfam00937 161 QSRGR-SGSNGQDDLVAAVLQALKELGVKKEGKKGKSTPKKRTKSAAARTKPkqlnKPRWKRTPNKGENVTQCFGPRSPG 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255 281 QtqgNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAY 360
Cdd:pfam00937 240 K---NFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKEQGDDVELTYTYKIKVPKDNPNLERFLEQLNAYVDPY 316

                         330       340
                  ....*....|....*....|....*...
gi 1798174255 361 KTFPPTEPKKDKKKKADETQAlPQRQKK 388
Cdd:pfam00937 317 KEFPPKPQKKKKKQSKLKPQA-PAFTPK 343
CoV_N-NTD cd21554
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 50-173 5.01e-53

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: 172.77  E-value: 5.01e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255  50 ASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGdGKMKDLSPRWYFYYLGTGPEAGLPYGANKDG 129
Cdd:cd21554     3 LSWFAPITQTGKNKPFFKVPQGVPPNGGGPKDQQIGYWNRQPRWRMGK-GGRKPLPPRWYFYYLGTGPHADLKYGERIDG 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1798174255 130 IIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGttLPKGFYA 173
Cdd:cd21554    82 VVWVAKEGADTNTPTDLGTRNPNNDEAIPLRFPPG--LPKGFYI 123
 
Name Accession Description Interval E-value
CoV_nucleocap pfam00937
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 46-388 2.18e-87

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: 269.22  E-value: 2.18e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255  46 PNNTASWFTALTQHG-KEDLKFPRGQGVPINTNSsPDDQIGYYRRATRrIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYG 124
Cdd:pfam00937   7 GRVPLSWFQPITQQGkKNFWKVMPGNGVPKGKGN-KDQQIGYWNRQPR-YRMGKGQRKQLPPRWYFYYLGTGPHANLKFG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255 125 ANKDGIIWVATEGALNTPKDHIGTRNPaNNAAIVLQLPQGttLPKGFYAEGSrGGSQASSRSSSRSRNSSRNSTPGSSRG 204
Cdd:pfam00937  85 ERIDGVFWVAKDGAKTSPTGKLGTRNP-NHEALPLRFPPG--LPKGFEIEGN-GRSRPNSRSQSRSRSRARSRSGSNSRS 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255 205 TSPARmAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASK----KPRQKRTATKAYNVTQAFGRRGPE 280
Cdd:pfam00937 161 QSRGR-SGSNGQDDLVAAVLQALKELGVKKEGKKGKSTPKKRTKSAAARTKPkqlnKPRWKRTPNKGENVTQCFGPRSPG 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255 281 QtqgNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAY 360
Cdd:pfam00937 240 K---NFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKEQGDDVELTYTYKIKVPKDNPNLERFLEQLNAYVDPY 316

                         330       340
                  ....*....|....*....|....*...
gi 1798174255 361 KTFPPTEPKKDKKKKADETQAlPQRQKK 388
Cdd:pfam00937 317 KEFPPKPQKKKKKQSKLKPQA-PAFTPK 343
CoV_N-NTD cd21554
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 50-173 5.01e-53

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: 172.77  E-value: 5.01e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255  50 ASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGdGKMKDLSPRWYFYYLGTGPEAGLPYGANKDG 129
Cdd:cd21554     3 LSWFAPITQTGKNKPFFKVPQGVPPNGGGPKDQQIGYWNRQPRWRMGK-GGRKPLPPRWYFYYLGTGPHADLKYGERIDG 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1798174255 130 IIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGttLPKGFYA 173
Cdd:cd21554    82 VVWVAKEGADTNTPTDLGTRNPNNDEAIPLRFPPG--LPKGFYI 123
CoV_N-CTD cd21595
C-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 269-359 3.84e-34

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: 122.20  E-value: 3.84e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1798174255 269 NVTQAFGRRGPEqtqGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKd 348
Cdd:cd21595     1 NVTQCFGPRGPE---GNFGDADLVKLGVDDPRFPQLAELVPSPAALLFGSHVSTKEQGDGVELTYTYKIKVPKDDKNLK- 76

                          90
                  ....*....|.
gi 1798174255 349 qviLLNKHIDA 359
Cdd:cd21595    77 ---AFLEQVDA 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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