NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|212681394|ref|YP_002308510|]
View 

nucleocapsid phosphoprotein [Munia coronavirus HKU13-3514]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 1-317 5.26e-92

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: 278.47  E-value: 5.26e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394    1 MATPAVPTTDASWFQVLKAQNKKAIHPQFKGNGVPVNSAiKPAENHGYWLRFARQKPGGAQ---IPPSYAFYYTGTGPRG 77
Cdd:pfam00937   1 MAPRRNGRVPLSWFQPITQQGKKNFWKVMPGNGVPKGKG-NKDQQIGYWNRQPRYRMGKGQrkqLPPRWYFYYLGTGPHA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394   78 NLKYGEYPPndsketsRITWVKGPGADTTIKPHVAKRNPNnpkHQLLPLRFPPgdGPAAGF------RVDPFN-SRGRTM 150
Cdd:pfam00937  80 NLKFGERID-------GVFWVAKDGAKTSPTGKLGTRNPN---HEALPLRFPP--GLPKGFeiegngRSRPNSrSQSRSR 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394  151 ERGNG-----PRSQSANDRPVQ--------------------------NQPKRRDRSAPAAVRRKT-QHQAPKRTLLKGK 198
Cdd:pfam00937 148 SRARSrsgsnSRSQSRGRSGSNgqddlvaavlqalkelgvkkegkkgkSTPKKRTKSAAARTKPKQlNKPRWKRTPNKGE 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394  199 TISQVFGTRSkAGANVGSADSEKAGMADSRIMTLARFVPGVQELLFAGHLDSNFQQDGaLTLTFTYSITVKQDSPDYDRL 278
Cdd:pfam00937 228 NVTQCFGPRS-PGKNFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKEQGDD-VELTYTYKIKVPKDNPNLERF 305

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 212681394  279 KDALNTVVNQTYEAPTKPQKVKKPESEQSSKPKQpRKPK 317
Cdd:pfam00937 306 LEQLNAYVDPYKEFPPKPQKKKKKQSKLKPQAPA-FTPK 343
 
Name Accession Description Interval E-value
CoV_nucleocap pfam00937
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 1-317 5.26e-92

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: 278.47  E-value: 5.26e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394    1 MATPAVPTTDASWFQVLKAQNKKAIHPQFKGNGVPVNSAiKPAENHGYWLRFARQKPGGAQ---IPPSYAFYYTGTGPRG 77
Cdd:pfam00937   1 MAPRRNGRVPLSWFQPITQQGKKNFWKVMPGNGVPKGKG-NKDQQIGYWNRQPRYRMGKGQrkqLPPRWYFYYLGTGPHA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394   78 NLKYGEYPPndsketsRITWVKGPGADTTIKPHVAKRNPNnpkHQLLPLRFPPgdGPAAGF------RVDPFN-SRGRTM 150
Cdd:pfam00937  80 NLKFGERID-------GVFWVAKDGAKTSPTGKLGTRNPN---HEALPLRFPP--GLPKGFeiegngRSRPNSrSQSRSR 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394  151 ERGNG-----PRSQSANDRPVQ--------------------------NQPKRRDRSAPAAVRRKT-QHQAPKRTLLKGK 198
Cdd:pfam00937 148 SRARSrsgsnSRSQSRGRSGSNgqddlvaavlqalkelgvkkegkkgkSTPKKRTKSAAARTKPKQlNKPRWKRTPNKGE 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394  199 TISQVFGTRSkAGANVGSADSEKAGMADSRIMTLARFVPGVQELLFAGHLDSNFQQDGaLTLTFTYSITVKQDSPDYDRL 278
Cdd:pfam00937 228 NVTQCFGPRS-PGKNFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKEQGDD-VELTYTYKIKVPKDNPNLERF 305

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 212681394  279 KDALNTVVNQTYEAPTKPQKVKKPESEQSSKPKQpRKPK 317
Cdd:pfam00937 306 LEQLNAYVDPYKEFPPKPQKKKKKQSKLKPQAPA-FTPK 343
CoV_N-NTD cd21554
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 9-140 1.78e-40

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: 138.49  E-value: 1.78e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394   9 TDASWFQVLKAQNKKaiHPQFK-GNGVPVNSAIKPAENHGYWLRFARQKPGGA---QIPPSYAFYYTGTGPRGNLKYGEY 84
Cdd:cd21554    1 IPLSWFAPITQTGKN--KPFFKvPQGVPPNGGGPKDQQIGYWNRQPRWRMGKGgrkPLPPRWYFYYLGTGPHADLKYGER 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 212681394  85 PPndsketsRITWVKGPGADTTIKPHVAKRNPNNpkHQLLPLRFPPgdGPAAGFRV 140
Cdd:cd21554   79 ID-------GVVWVAKEGADTNTPTDLGTRNPNN--DEAIPLRFPP--GLPKGFYI 123
 
Name Accession Description Interval E-value
CoV_nucleocap pfam00937
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 1-317 5.26e-92

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: 278.47  E-value: 5.26e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394    1 MATPAVPTTDASWFQVLKAQNKKAIHPQFKGNGVPVNSAiKPAENHGYWLRFARQKPGGAQ---IPPSYAFYYTGTGPRG 77
Cdd:pfam00937   1 MAPRRNGRVPLSWFQPITQQGKKNFWKVMPGNGVPKGKG-NKDQQIGYWNRQPRYRMGKGQrkqLPPRWYFYYLGTGPHA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394   78 NLKYGEYPPndsketsRITWVKGPGADTTIKPHVAKRNPNnpkHQLLPLRFPPgdGPAAGF------RVDPFN-SRGRTM 150
Cdd:pfam00937  80 NLKFGERID-------GVFWVAKDGAKTSPTGKLGTRNPN---HEALPLRFPP--GLPKGFeiegngRSRPNSrSQSRSR 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394  151 ERGNG-----PRSQSANDRPVQ--------------------------NQPKRRDRSAPAAVRRKT-QHQAPKRTLLKGK 198
Cdd:pfam00937 148 SRARSrsgsnSRSQSRGRSGSNgqddlvaavlqalkelgvkkegkkgkSTPKKRTKSAAARTKPKQlNKPRWKRTPNKGE 227

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394  199 TISQVFGTRSkAGANVGSADSEKAGMADSRIMTLARFVPGVQELLFAGHLDSNFQQDGaLTLTFTYSITVKQDSPDYDRL 278
Cdd:pfam00937 228 NVTQCFGPRS-PGKNFGDADLVKLGVDDPRFPQLAELVPGPAALLFGSHVETKEQGDD-VELTYTYKIKVPKDNPNLERF 305

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 212681394  279 KDALNTVVNQTYEAPTKPQKVKKPESEQSSKPKQpRKPK 317
Cdd:pfam00937 306 LEQLNAYVDPYKEFPPKPQKKKKKQSKLKPQAPA-FTPK 343
CoV_N-NTD cd21554
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 9-140 1.78e-40

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: 138.49  E-value: 1.78e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394   9 TDASWFQVLKAQNKKaiHPQFK-GNGVPVNSAIKPAENHGYWLRFARQKPGGA---QIPPSYAFYYTGTGPRGNLKYGEY 84
Cdd:cd21554    1 IPLSWFAPITQTGKN--KPFFKvPQGVPPNGGGPKDQQIGYWNRQPRWRMGKGgrkPLPPRWYFYYLGTGPHADLKYGER 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 212681394  85 PPndsketsRITWVKGPGADTTIKPHVAKRNPNNpkHQLLPLRFPPgdGPAAGFRV 140
Cdd:cd21554   79 ID-------GVVWVAKEGADTNTPTDLGTRNPNN--DEAIPLRFPP--GLPKGFYI 123
CoV_N-CTD cd21595
C-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 199-288 8.25e-26

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: 98.71  E-value: 8.25e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212681394 199 TISQVFGTRSKaGANVGSADSEKAGMADSRIMTLARFVPGVQELLFAGHLDSNFQQDGaLTLTFTYSITVKQDspdyDRL 278
Cdd:cd21595    1 NVTQCFGPRGP-EGNFGDADLVKLGVDDPRFPQLAELVPSPAALLFGSHVSTKEQGDG-VELTYTYKIKVPKD----DKN 74

                         90
                 ....*....|
gi 212681394 279 KDALNTVVNQ 288
Cdd:cd21595   75 LKAFLEQVDA 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH