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Conserved domains on  [gi|1802476813|ref|YP_009725305|]
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nsp9 [Severe acute respiratory syndrome coronavirus 2]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
betaCoV_Nsp9 cd21898
betacoronavirus non-structural protein 9; This model represents the non-structural protein 9 ...
 1-113 5.27e-65

betacoronavirus non-structural protein 9; This model represents the non-structural protein 9 (Nsp9) from betacoronaviruses including highly pathogenic Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. All of these Nsps, except for Nsp1 and Nsp2, are considered essential for transcription, replication, and translation of the viral RNA. Nsp9, with Nsp7, Nsp8, and Nsp10, localizes within the replication complex. Nsp9 is an essential single-stranded RNA-binding protein for coronavirus replication; it shares structural similarity to the oligosaccharide-binding (OB) fold, which is characteristic of proteins that bind to ssDNA or ssRNA. Nsp9 requires dimerization for binding and orienting RNA for subsequent use by the replicase machinery. CoV Nsp9s have diverse forms of dimerization that promote their biological function, which may help elucidate the mechanism underlying CoVs replication and contribute to the development of antiviral drugs. Generally, dimers are formed via interaction of the parallel alpha-helices containing the protein-protein interaction motif GXXXG; additionally, the N-finger region may also play a critical role in dimerization as seen in porcine delta coronavirus (PDCoV) Nsp9. As a member of the replication complex, Nsp9 may not have a specific RNA-binding sequence but may act in conjunction with other Nsps as a processivity factor, as shown by mutation studies indicating that Nsp9 is a key ingredient that intimately engages other proteins in the replicase complex to mediate efficient virus transcription and replication.


:

Pssm-ID: 409331  Cd Length: 111  Bit Score: 191.84  E-value: 5.27e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476813   1 NNELSPVALRQMSCAAGTTQTACtDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGtGTIYTELEPPCRFVTDTP 80
Cdd:cd21898     1 NNELMPQGLKTMVVTAGPDQTAC-NTPALAYYNNVQGGRMVMAILSDVDGLKYAKVEKSDG-GFVVLELDPPCKFLVQTP 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1802476813  81 KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
Cdd:cd21898    79 KGPKVKYLYFVKGLNNLHRGQVLGTIAATVRLQ 111
 
Name Accession Description Interval E-value
betaCoV_Nsp9 cd21898
betacoronavirus non-structural protein 9; This model represents the non-structural protein 9 ...
 1-113 5.27e-65

betacoronavirus non-structural protein 9; This model represents the non-structural protein 9 (Nsp9) from betacoronaviruses including highly pathogenic Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. All of these Nsps, except for Nsp1 and Nsp2, are considered essential for transcription, replication, and translation of the viral RNA. Nsp9, with Nsp7, Nsp8, and Nsp10, localizes within the replication complex. Nsp9 is an essential single-stranded RNA-binding protein for coronavirus replication; it shares structural similarity to the oligosaccharide-binding (OB) fold, which is characteristic of proteins that bind to ssDNA or ssRNA. Nsp9 requires dimerization for binding and orienting RNA for subsequent use by the replicase machinery. CoV Nsp9s have diverse forms of dimerization that promote their biological function, which may help elucidate the mechanism underlying CoVs replication and contribute to the development of antiviral drugs. Generally, dimers are formed via interaction of the parallel alpha-helices containing the protein-protein interaction motif GXXXG; additionally, the N-finger region may also play a critical role in dimerization as seen in porcine delta coronavirus (PDCoV) Nsp9. As a member of the replication complex, Nsp9 may not have a specific RNA-binding sequence but may act in conjunction with other Nsps as a processivity factor, as shown by mutation studies indicating that Nsp9 is a key ingredient that intimately engages other proteins in the replicase complex to mediate efficient virus transcription and replication.


Pssm-ID: 409331  Cd Length: 111  Bit Score: 191.84  E-value: 5.27e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476813   1 NNELSPVALRQMSCAAGTTQTACtDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGtGTIYTELEPPCRFVTDTP 80
Cdd:cd21898     1 NNELMPQGLKTMVVTAGPDQTAC-NTPALAYYNNVQGGRMVMAILSDVDGLKYAKVEKSDG-GFVVLELDPPCKFLVQTP 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1802476813  81 KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
Cdd:cd21898    79 KGPKVKYLYFVKGLNNLHRGQVLGTIAATVRLQ 111
CoV_NSP9 pfam08710
Coronavirus replicase NSP9; Nsp9 is a single-stranded RNA-binding viral protein involved in ...
 1-113 5.12e-62

Coronavirus replicase NSP9; Nsp9 is a single-stranded RNA-binding viral protein involved in RNA synthesis. Several crystallographic structures of nsp9 have shown that it is composed of seven beta strands and a single alpha helix. Nsp9 proteins have N-finger motifs and highly conserved GXXXG motifs that both play critical roles in dimerization. The conserved helix-helix dimer interface containing a GXXXG protein-protein interaction motif is biologically relevant to SARS-CoV replication.


Pssm-ID: 285872  Cd Length: 111  Bit Score: 184.60  E-value: 5.12e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476813   1 NNELSPVALRQMSCAAGTTQtACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTgTIYTELEPPCRFVTDTP 80
Cdd:pfam08710   1 NNELMPGKLKTKACKAGVTD-AHCSVEGKAYYNNEGGGSFVYAILSSNPNLKYAKFEKEDGN-VIYVELEPPCRFVVDTP 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1802476813  81 KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
Cdd:pfam08710  79 KGPEVKYLYFVKNLNNLRRGMVLGYISATVRLQ 111
 
Name Accession Description Interval E-value
betaCoV_Nsp9 cd21898
betacoronavirus non-structural protein 9; This model represents the non-structural protein 9 ...
 1-113 5.27e-65

betacoronavirus non-structural protein 9; This model represents the non-structural protein 9 (Nsp9) from betacoronaviruses including highly pathogenic Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. All of these Nsps, except for Nsp1 and Nsp2, are considered essential for transcription, replication, and translation of the viral RNA. Nsp9, with Nsp7, Nsp8, and Nsp10, localizes within the replication complex. Nsp9 is an essential single-stranded RNA-binding protein for coronavirus replication; it shares structural similarity to the oligosaccharide-binding (OB) fold, which is characteristic of proteins that bind to ssDNA or ssRNA. Nsp9 requires dimerization for binding and orienting RNA for subsequent use by the replicase machinery. CoV Nsp9s have diverse forms of dimerization that promote their biological function, which may help elucidate the mechanism underlying CoVs replication and contribute to the development of antiviral drugs. Generally, dimers are formed via interaction of the parallel alpha-helices containing the protein-protein interaction motif GXXXG; additionally, the N-finger region may also play a critical role in dimerization as seen in porcine delta coronavirus (PDCoV) Nsp9. As a member of the replication complex, Nsp9 may not have a specific RNA-binding sequence but may act in conjunction with other Nsps as a processivity factor, as shown by mutation studies indicating that Nsp9 is a key ingredient that intimately engages other proteins in the replicase complex to mediate efficient virus transcription and replication.


Pssm-ID: 409331  Cd Length: 111  Bit Score: 191.84  E-value: 5.27e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476813   1 NNELSPVALRQMSCAAGTTQTACtDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGtGTIYTELEPPCRFVTDTP 80
Cdd:cd21898     1 NNELMPQGLKTMVVTAGPDQTAC-NTPALAYYNNVQGGRMVMAILSDVDGLKYAKVEKSDG-GFVVLELDPPCKFLVQTP 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1802476813  81 KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
Cdd:cd21898    79 KGPKVKYLYFVKGLNNLHRGQVLGTIAATVRLQ 111
CoV_Nsp9 cd21881
coronavirus non-structural protein 9; This model represents the non-structural protein 9 (Nsp9) ...
 1-113 4.24e-62

coronavirus non-structural protein 9; This model represents the non-structural protein 9 (Nsp9) from coronaviruses, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. All of these Nsps, except for Nsp1 and Nsp2, are considered essential for transcription, replication, and translation of the viral RNA. Nsp9, with Nsp7, Nsp8, and Nsp10, localizes within the replication complex. Nsp9 is an essential single-stranded RNA-binding protein for CoV replication; it shares structural similarity to the oligosaccharide-binding (OB) fold, which is characteristic of proteins that bind to ssDNA or ssRNA. Nsp9 requires dimerization for binding and orienting RNA for subsequent use by the replicase machinery. CoV Nsp9s have diverse forms of dimerization that promote their biological function, which may help elucidate the mechanism underlying CoVs replication and contribute to the development of antiviral drugs. Generally, dimers are formed via interaction of the parallel alpha-helices containing the protein-protein interaction motif GXXXG at the C-terminus; additionally, the N-finger region may also play a critical role in dimerization as seen in porcine delta coronavirus (PDCoV) Nsp9. As a member of the replication complex, Nsp9 may not have a specific RNA-binding sequence but may act in conjunction with other Nsps as a processivity factor, as shown by mutation studies indicating that Nsp9 is a key ingredient that intimately engages other proteins in the replicase complex to mediate efficient virus transcription and replication.


Pssm-ID: 409329  Cd Length: 111  Bit Score: 184.64  E-value: 4.24e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476813   1 NNELSPVALRQMSCAAGTTQTaCTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGtGTIYTELEPPCRFVTDTP 80
Cdd:cd21881     1 NNELSPVALKQMSCAAGTDQT-CTDDEAKAYYNNSKGGRFVLAITSDKPDLKVARFLKEDG-GTIYTELEPPCRFVTDVP 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1802476813  81 KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
Cdd:cd21881    79 KGPKVKYLYFIKNLNSLNRGMVLGSISATVRLQ 111
CoV_NSP9 pfam08710
Coronavirus replicase NSP9; Nsp9 is a single-stranded RNA-binding viral protein involved in ...
 1-113 5.12e-62

Coronavirus replicase NSP9; Nsp9 is a single-stranded RNA-binding viral protein involved in RNA synthesis. Several crystallographic structures of nsp9 have shown that it is composed of seven beta strands and a single alpha helix. Nsp9 proteins have N-finger motifs and highly conserved GXXXG motifs that both play critical roles in dimerization. The conserved helix-helix dimer interface containing a GXXXG protein-protein interaction motif is biologically relevant to SARS-CoV replication.


Pssm-ID: 285872  Cd Length: 111  Bit Score: 184.60  E-value: 5.12e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476813   1 NNELSPVALRQMSCAAGTTQtACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTgTIYTELEPPCRFVTDTP 80
Cdd:pfam08710   1 NNELMPGKLKTKACKAGVTD-AHCSVEGKAYYNNEGGGSFVYAILSSNPNLKYAKFEKEDGN-VIYVELEPPCRFVVDTP 78

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1802476813  81 KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
Cdd:pfam08710  79 KGPEVKYLYFVKNLNNLRRGMVLGYISATVRLQ 111
alphaCoV_Nsp9 cd21897
alphacoronavirus non-structural protein 9; This model represents the non-structural protein 9 ...
 1-113 3.43e-35

alphacoronavirus non-structural protein 9; This model represents the non-structural protein 9 (Nsp9) of alphacoronaviruses, including Porcine epidemic diarrhea virus (PEDV), Porcine transmissible gastroenteritis coronavirus (TGEV), and Human coronavirus 229E. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. All of these Nsps, except for Nsp1 and Nsp2, are considered essential for transcription, replication, and translation of the viral RNA. Nsp9, with Nsp7, Nsp8, and Nsp10, localizes within the replication complex. Nsp9 is an essential single-stranded RNA-binding protein for coronavirus replication; it shares structural similarity to the oligosaccharide-binding (OB) fold, which is characteristic of proteins that bind to ssDNA or ssRNA. Nsp9 requires dimerization for binding and orienting RNA for subsequent use by the replicase machinery. CoV Nsp9s have diverse forms of dimerization that promote their biological function, which may help elucidate the mechanism underlying CoVs replication and contribute to the development of antiviral drugs. Generally, dimers are formed via interaction of the parallel alpha-helices containing the protein-protein interaction motif GXXXG; additionally, the N-finger region may also play a critical role in dimerization as seen in porcine delta coronavirus (PDCoV) Nsp9. As a member of the replication complex, Nsp9 may not have a specific RNA-binding sequence but may act in conjunction with other Nsps as a processivity factor, as shown by mutation studies indicating that Nsp9 is a key ingredient that intimately engages other proteins in the replicase complex to mediate efficient virus transcription and replication.


Pssm-ID: 409330  Cd Length: 108  Bit Score: 116.65  E-value: 3.43e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476813   1 NNELSPVALRQMSCAAGTTqTACTDDNALayYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIytELEPPCRFVTDTP 80
Cdd:cd21897     1 NNEIMPGKLKQRAVKAEGD-GFSGDGKAL--YNNEGGKTFMYAFIADKPDLKYVKWEFDGGCNTI--ELEPPCKFLVDTP 75

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1802476813  81 KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
Cdd:cd21897    76 NGPQIKYLYFVKNLNTLRRGAVLGYIGATVRLQ 108
gammaCoV_Nsp9 cd21899
gammacoronavirus non-structural protein 9; This model represents the non-structural protein 9 ...
 1-113 5.29e-26

gammacoronavirus non-structural protein 9; This model represents the non-structural protein 9 (Nsp9) from gammacoronaviruses such as Avian infectious bronchitis virus (IBV). CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. All of these Nsps, except for Nsp1 and Nsp2, are considered essential for transcription, replication, and translation of the viral RNA. Nsp9, with Nsp7, Nsp8, and Nsp10, localizes within the replication complex. Nsp9 is an essential single-stranded RNA-binding protein for coronavirus replication; it shares structural similarity to the oligosaccharide-binding (OB) fold, which is characteristic of proteins that bind to ssDNA or ssRNA. Nsp9 requires dimerization for binding and orienting RNA for subsequent use by the replicase machinery. CoV Nsp9s have diverse forms of dimerization that promote their biological function, which may help elucidate the mechanism underlying CoVs replication and contribute to the development of antiviral drugs. Generally, dimers are formed via interaction of the parallel alpha-helices containing the protein-protein interaction motif GXXXG; additionally, the N-finger region may also play a critical role in dimerization as seen in porcine delta coronavirus (PDCoV) Nsp9. As a member of the replication complex, Nsp9 may not have a specific RNA-binding sequence but may act in conjunction with other Nsps as a processivity factor, as shown by mutation studies indicating that Nsp9 is a key ingredient that intimately engages other proteins in the replicase complex to mediate efficient virus transcription and replication.


Pssm-ID: 409332  Cd Length: 113  Bit Score: 93.38  E-value: 5.29e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476813   1 NNELSPVALRQMSCAAGTTQTACTDDnALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTgTIYTELEPPCRFVTDTP 80
Cdd:cd21899     3 NNELMPHGVKTKACVAGVDQAHCSVE-SKCYYTNISGNSVVAAITSSNPNLKVASFLNEAGN-QIYVDLDPPCKFGMKVG 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1802476813  81 KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
Cdd:cd21899    81 DKVEVVYLYFIKNTRSIVRGMVLGAISNVVVLQ 113
deltaCoV_Nsp9 cd21900
deltacoronavirus non-structural protein 9; This model represents the non-structural protein 9 ...
 1-113 1.16e-18

deltacoronavirus non-structural protein 9; This model represents the non-structural protein 9 (Nsp9) from deltacoronaviruses such as the Porcine delta coronavirus (PDCoV) Porcine coronavirus HKU15. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. All of these Nsps, except for Nsp1 and Nsp2, are considered essential for transcription, replication, and translation of the viral RNA. Nsp9, with Nsp7, Nsp8, and Nsp10, localizes within the replication complex. Nsp9 is an essential single-stranded RNA-binding protein for coronavirus replication; it shares structural similarity to the oligosaccharide-binding (OB) fold, which is characteristic of proteins that bind to ssDNA or ssRNA. Nsp9 requires dimerization for binding and orienting RNA for subsequent use by the replicase machinery. CoV Nsp9s have diverse forms of dimerization that promote their biological function, which may help elucidate the mechanism underlying CoVs replication and contribute to the development of antiviral drugs. Generally, dimers are formed via interaction of the parallel alpha-helices containing the protein-protein interaction motif GXXXG; additionally, the N-finger region may also play a critical role in dimerization as seen in porcine delta coronavirus (PDCoV) Nsp9. As a member of the replication complex, Nsp9 may not have a specific RNA-binding sequence but may act in conjunction with other Nsps as a processivity factor, as shown by mutation studies indicating that Nsp9 is a key ingredient that intimately engages other proteins in the replicase complex to mediate efficient virus transcription and replication.


Pssm-ID: 409333  Cd Length: 109  Bit Score: 74.39  E-value: 1.16e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476813   1 NNELspvALRQMSCAagttQTACTDDN-----ALAYYNTTKGGRFVLALLSDLQDLKWArFPKSDgTGTIYTELEPPCRF 75
Cdd:cd21900     1 NNEL---CLRNVFTA----QNTASDGNgnestAKSFYVSRTGKKILVAVTSTKDNLKTV-TCDTD-TGKVVLNLDPPMRF 71

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1802476813  76 -VTDTPKgPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ 113
Cdd:cd21900    72 sHVVGGK-QSVVYLYFIQNISSLNRGMVIGHISGTTILQ 109
 
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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