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Conserved domains on  [gi|2754671107|gb|XCM62864|]
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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 ...
 43-385 1.08e-86

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: 267.29  E-value: 1.08e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107  43 PNNTASWFTALTQHG-KEDLKFPRGQGVPINTNSsPDDQIGYYRRATRrIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYG 121
Cdd:pfam00937   7 GRVPLSWFQPITQQGkKNFWKVMPGNGVPKGKGN-KDQQIGYWNRQPR-YRMGKGQRKQLPPRWYFYYLGTGPHANLKFG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107 122 ANKDGIIWVATEGALNTPKDHIGTRNPaNNAAIVLQLPQGttLPKGFYAEG-----------SRGGSQASSRSssrsrns 190
Cdd:pfam00937  85 ERIDGVFWVAKDGAKTSPTGKLGTRNP-NHEALPLRFPPG--LPKGFEIEGngrsrpnsrsqSRSRSRARSRS------- 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107 191 srnstpGSSKRTSPARMAGNGGDAALALLLLDRLNKLESKMSGKGQQQQGQTVTKKSAAEASK----KPRQKRTATKAYN 266
Cdd:pfam00937 155 ------GSNSRSQSRGRSGSNGQDDLVAAVLQALKELGVKKEGKKGKSTPKKRTKSAAARTKPkqlnKPRWKRTPNKGEN 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107 267 VTQAFGRRGPEQtqgNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQ 346
Cdd:pfam00937 229 VTQCFGPRSPGK---NFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKEQGDDVELTYTYKIKVPKDNPNLERF 305

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 2754671107 347 VILLNKHIDAYKTFPPTEPKKDKKKKADETQAlPQRQKK 385
Cdd:pfam00937 306 LEQLNAYVDPYKEFPPKPQKKKKKQSKLKPQA-PAFTPK 343
 
Name Accession Description Interval E-value
CoV_nucleocap pfam00937
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 43-385 1.08e-86

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: 267.29  E-value: 1.08e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107  43 PNNTASWFTALTQHG-KEDLKFPRGQGVPINTNSsPDDQIGYYRRATRrIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYG 121
Cdd:pfam00937   7 GRVPLSWFQPITQQGkKNFWKVMPGNGVPKGKGN-KDQQIGYWNRQPR-YRMGKGQRKQLPPRWYFYYLGTGPHANLKFG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107 122 ANKDGIIWVATEGALNTPKDHIGTRNPaNNAAIVLQLPQGttLPKGFYAEG-----------SRGGSQASSRSssrsrns 190
Cdd:pfam00937  85 ERIDGVFWVAKDGAKTSPTGKLGTRNP-NHEALPLRFPPG--LPKGFEIEGngrsrpnsrsqSRSRSRARSRS------- 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107 191 srnstpGSSKRTSPARMAGNGGDAALALLLLDRLNKLESKMSGKGQQQQGQTVTKKSAAEASK----KPRQKRTATKAYN 266
Cdd:pfam00937 155 ------GSNSRSQSRGRSGSNGQDDLVAAVLQALKELGVKKEGKKGKSTPKKRTKSAAARTKPkqlnKPRWKRTPNKGEN 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107 267 VTQAFGRRGPEQtqgNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQ 346
Cdd:pfam00937 229 VTQCFGPRSPGK---NFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKEQGDDVELTYTYKIKVPKDNPNLERF 305

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 2754671107 347 VILLNKHIDAYKTFPPTEPKKDKKKKADETQAlPQRQKK 385
Cdd:pfam00937 306 LEQLNAYVDPYKEFPPKPQKKKKKQSKLKPQA-PAFTPK 343
CoV_N-NTD cd21554
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 47-170 4.42e-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: 4.42e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107  47 ASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGdGKMKDLSPRWYFYYLGTGPEAGLPYGANKDG 126
Cdd:cd21554     3 LSWFAPITQTGKNKPFFKVPQGVPPNGGGPKDQQIGYWNRQPRWRMGK-GGRKPLPPRWYFYYLGTGPHADLKYGERIDG 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2754671107 127 IIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGttLPKGFYA 170
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 ...
 43-385 1.08e-86

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: 267.29  E-value: 1.08e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107  43 PNNTASWFTALTQHG-KEDLKFPRGQGVPINTNSsPDDQIGYYRRATRrIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYG 121
Cdd:pfam00937   7 GRVPLSWFQPITQQGkKNFWKVMPGNGVPKGKGN-KDQQIGYWNRQPR-YRMGKGQRKQLPPRWYFYYLGTGPHANLKFG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107 122 ANKDGIIWVATEGALNTPKDHIGTRNPaNNAAIVLQLPQGttLPKGFYAEG-----------SRGGSQASSRSssrsrns 190
Cdd:pfam00937  85 ERIDGVFWVAKDGAKTSPTGKLGTRNP-NHEALPLRFPPG--LPKGFEIEGngrsrpnsrsqSRSRSRARSRS------- 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107 191 srnstpGSSKRTSPARMAGNGGDAALALLLLDRLNKLESKMSGKGQQQQGQTVTKKSAAEASK----KPRQKRTATKAYN 266
Cdd:pfam00937 155 ------GSNSRSQSRGRSGSNGQDDLVAAVLQALKELGVKKEGKKGKSTPKKRTKSAAARTKPkqlnKPRWKRTPNKGEN 228

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107 267 VTQAFGRRGPEQtqgNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQ 346
Cdd:pfam00937 229 VTQCFGPRSPGK---NFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKEQGDDVELTYTYKIKVPKDNPNLERF 305

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 2754671107 347 VILLNKHIDAYKTFPPTEPKKDKKKKADETQAlPQRQKK 385
Cdd:pfam00937 306 LEQLNAYVDPYKEFPPKPQKKKKKQSKLKPQA-PAFTPK 343
CoV_N-NTD cd21554
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 47-170 4.42e-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: 4.42e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107  47 ASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGdGKMKDLSPRWYFYYLGTGPEAGLPYGANKDG 126
Cdd:cd21554     3 LSWFAPITQTGKNKPFFKVPQGVPPNGGGPKDQQIGYWNRQPRWRMGK-GGRKPLPPRWYFYYLGTGPHADLKYGERIDG 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2754671107 127 IIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGttLPKGFYA 170
Cdd:cd21554    82 VVWVAKEGADTNTPTDLGTRNPNNDEAIPLRFPPG--LPKGFYI 123
CoV_N-CTD cd21595
C-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 266-356 3.77e-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: 3.77e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2754671107 266 NVTQAFGRRGPEqtqGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKd 345
Cdd:cd21595     1 NVTQCFGPRGPE---GNFGDADLVKLGVDDPRFPQLAELVPSPAALLFGSHVSTKEQGDGVELTYTYKIKVPKDDKNLK- 76

                          90
                  ....*....|.
gi 2754671107 346 qviLLNKHIDA 356
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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