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Conserved domains on  [gi|744692662|ref|YP_009113031|]
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nucleocapsid protein [Betacoronavirus HKU24]

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 ...
 49-411 5.03e-114

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: 338.17  E-value: 5.03e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662   49 QASGGNVVPFYSWFSGITQFQKGQEFGFEQGQGVPLTNGvPPSEEKGYWYRHNRksYRTADGQQRQLLPRWYFYYLGTGP 128
Cdd:pfam00937   1 MAPRRNGRVPLSWFQPITQQGKKNFWKVMPGNGVPKGKG-NKDQQIGYWNRQPR--YRMGKGQRKQLPPRWYFYYLGTGP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662  129 YANKQYGSDIDGVVWVASPNVDVRSPADVPDRDPtSHQAEPTRFAPGtvLPKGYYVEGSGRSAPSSRSSSRASSRASSVG 208
Cdd:pfam00937  78 HANLKFGERIDGVFWVAKDGAKTSPTGKLGTRNP-NHEALPLRFPPG--LPKGFEIEGNGRSRPNSRSQSRSRSRARSRS 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662  209 GSRSRNNSASRNNTS---EVTPDMADQIASLVLAKLNKE-SGKPVQVTKQTAKEIKQKILNKPRQKRTPNKQCTVQQCFG 284
Cdd:pfam00937 155 GSNSRSQSRGRSGSNgqdDLVAAVLQALKELGVKKEGKKgKSTPKKRTKSAAARTKPKQLNKPRWKRTPNKGENVTQCFG 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662  285 KRGPSQNFGGGSMLKLGTSDPQFPILAELAPTAGAFFFGSKLELAKvnnmsgaadepQKDVYELRYSGAIRFDSTLPGFE 364
Cdd:pfam00937 235 PRSPGKNFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKE-----------QGDDVELTYTYKIKVPKDNPNLE 303

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 744692662  365 TIMKVMNENLDAYqhteegaQLLSPKFQRKQKKGQVEKDNVSAATPK 411
Cdd:pfam00937 304 RFLEQLNAYVDPY-------KEFPPKPQKKKKKQSKLKPQAPAFTPK 343
 
Name Accession Description Interval E-value
CoV_nucleocap pfam00937
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 49-411 5.03e-114

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: 338.17  E-value: 5.03e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662   49 QASGGNVVPFYSWFSGITQFQKGQEFGFEQGQGVPLTNGvPPSEEKGYWYRHNRksYRTADGQQRQLLPRWYFYYLGTGP 128
Cdd:pfam00937   1 MAPRRNGRVPLSWFQPITQQGKKNFWKVMPGNGVPKGKG-NKDQQIGYWNRQPR--YRMGKGQRKQLPPRWYFYYLGTGP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662  129 YANKQYGSDIDGVVWVASPNVDVRSPADVPDRDPtSHQAEPTRFAPGtvLPKGYYVEGSGRSAPSSRSSSRASSRASSVG 208
Cdd:pfam00937  78 HANLKFGERIDGVFWVAKDGAKTSPTGKLGTRNP-NHEALPLRFPPG--LPKGFEIEGNGRSRPNSRSQSRSRSRARSRS 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662  209 GSRSRNNSASRNNTS---EVTPDMADQIASLVLAKLNKE-SGKPVQVTKQTAKEIKQKILNKPRQKRTPNKQCTVQQCFG 284
Cdd:pfam00937 155 GSNSRSQSRGRSGSNgqdDLVAAVLQALKELGVKKEGKKgKSTPKKRTKSAAARTKPKQLNKPRWKRTPNKGENVTQCFG 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662  285 KRGPSQNFGGGSMLKLGTSDPQFPILAELAPTAGAFFFGSKLELAKvnnmsgaadepQKDVYELRYSGAIRFDSTLPGFE 364
Cdd:pfam00937 235 PRSPGKNFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKE-----------QGDDVELTYTYKIKVPKDNPNLE 303

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 744692662  365 TIMKVMNENLDAYqhteegaQLLSPKFQRKQKKGQVEKDNVSAATPK 411
Cdd:pfam00937 304 RFLEQLNAYVDPY-------KEFPPKPQKKKKKQSKLKPQAPAFTPK 343
CoV_N-NTD cd21554
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 57-184 9.39e-56

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: 180.47  E-value: 9.39e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662  57 PFYSWFSGITQFQKGQEFgFEQGQGVPLTNGVPPSEEKGYWYRHNRKSYRTadGQQRQLLPRWYFYYLGTGPYANKQYGS 136
Cdd:cd21554    1 IPLSWFAPITQTGKNKPF-FKVPQGVPPNGGGPKDQQIGYWNRQPRWRMGK--GGRKPLPPRWYFYYLGTGPHADLKYGE 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 744692662 137 DIDGVVWVASPNVDVRSPADVPDRDPTSHQAEPTRFAPGtvLPKGYYV 184
Cdd:cd21554   78 RIDGVVWVAKEGADTNTPTDLGTRNPNNDEAIPLRFPPG--LPKGFYI 123
 
Name Accession Description Interval E-value
CoV_nucleocap pfam00937
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 49-411 5.03e-114

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: 338.17  E-value: 5.03e-114
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662   49 QASGGNVVPFYSWFSGITQFQKGQEFGFEQGQGVPLTNGvPPSEEKGYWYRHNRksYRTADGQQRQLLPRWYFYYLGTGP 128
Cdd:pfam00937   1 MAPRRNGRVPLSWFQPITQQGKKNFWKVMPGNGVPKGKG-NKDQQIGYWNRQPR--YRMGKGQRKQLPPRWYFYYLGTGP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662  129 YANKQYGSDIDGVVWVASPNVDVRSPADVPDRDPtSHQAEPTRFAPGtvLPKGYYVEGSGRSAPSSRSSSRASSRASSVG 208
Cdd:pfam00937  78 HANLKFGERIDGVFWVAKDGAKTSPTGKLGTRNP-NHEALPLRFPPG--LPKGFEIEGNGRSRPNSRSQSRSRSRARSRS 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662  209 GSRSRNNSASRNNTS---EVTPDMADQIASLVLAKLNKE-SGKPVQVTKQTAKEIKQKILNKPRQKRTPNKQCTVQQCFG 284
Cdd:pfam00937 155 GSNSRSQSRGRSGSNgqdDLVAAVLQALKELGVKKEGKKgKSTPKKRTKSAAARTKPKQLNKPRWKRTPNKGENVTQCFG 234

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662  285 KRGPSQNFGGGSMLKLGTSDPQFPILAELAPTAGAFFFGSKLELAKvnnmsgaadepQKDVYELRYSGAIRFDSTLPGFE 364
Cdd:pfam00937 235 PRSPGKNFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKE-----------QGDDVELTYTYKIKVPKDNPNLE 303

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 744692662  365 TIMKVMNENLDAYqhteegaQLLSPKFQRKQKKGQVEKDNVSAATPK 411
Cdd:pfam00937 304 RFLEQLNAYVDPY-------KEFPPKPQKKKKKQSKLKPQAPAFTPK 343
CoV_N-NTD cd21554
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 57-184 9.39e-56

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: 180.47  E-value: 9.39e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662  57 PFYSWFSGITQFQKGQEFgFEQGQGVPLTNGVPPSEEKGYWYRHNRKSYRTadGQQRQLLPRWYFYYLGTGPYANKQYGS 136
Cdd:cd21554    1 IPLSWFAPITQTGKNKPF-FKVPQGVPPNGGGPKDQQIGYWNRQPRWRMGK--GGRKPLPPRWYFYYLGTGPHADLKYGE 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 744692662 137 DIDGVVWVASPNVDVRSPADVPDRDPTSHQAEPTRFAPGtvLPKGYYV 184
Cdd:cd21554   78 RIDGVVWVAKEGADTNTPTDLGTRNPNNDEAIPLRFPPG--LPKGFYI 123
CoV_N-CTD cd21595
C-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 278-376 4.23e-28

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: 106.41  E-value: 4.23e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 744692662 278 TVQQCFGKRGPSQNFGGGSMLKLGTSDPQFPILAELAPTAGAFFFGSKLELAKvnnmsgaadepQKDVYELRYSGAIRFD 357
Cdd:cd21595    1 NVTQCFGPRGPEGNFGDADLVKLGVDDPRFPQLAELVPSPAALLFGSHVSTKE-----------QGDGVELTYTYKIKVP 69

                         90
                 ....*....|....*....
gi 744692662 358 STlpgfETIMKVMNENLDA 376
Cdd:cd21595   70 KD----DKNLKAFLEQVDA 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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