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Conserved domains on  [gi|1802476805|ref|YP_009725297|]
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leader protein [Severe acute respiratory syndrome coronavirus 2]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SARS-CoV-like_Nsp1_N cd21796
N-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related ...
 13-127 2.98e-80

N-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage; This model represents the N-terminal domain of non-structural protein 1 (Nsp1) from betacoronaviruses in the sarbecovirus subgenus (B lineage), including highly pathogenic coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). 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. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome.


:

Pssm-ID: 439285  Cd Length: 115  Bit Score: 233.63  E-value: 2.98e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476805  13 HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAEL 92
Cdd:cd21796     1 HVQLSLPVLQVRDVLVRGFGDSVEEALSEAREHLKNGTCGLVELEKGVLPQLEQPYVFIKRSDALSTNHGHKVVELVAEL 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1802476805  93 EGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNG 127
Cdd:cd21796    81 DGIQYGRSGITLGVLVPHVGETPIAYRNVLLRKNG 115
SARS-CoV-like_Nsp1_C super family cl45576
C-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related ...
 128-180 2.25e-32

C-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage; This model represents the C-terminal domain of non-structural protein 1 (Nsp1) from betacoronaviruses in the sarbecovirus subgenus (B lineage), including highly pathogenic coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). 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. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression. SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome. When the SARS-CoV-2 5' UTR is bound to the Nsp1 N-terminus, the covalently linked Nsp1 C-terminus cannot bind the 40S ribosome, suggesting a bipartite mechanism whereby SARS-CoV-2 Nsp1 suppresses host but not viral translation.


The actual alignment was detected with superfamily member cd22662:

Pssm-ID: 439355  Cd Length: 53  Bit Score: 110.34  E-value: 2.25e-32
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1802476805 128 NKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG 180
Cdd:cd22662     1 NKGAGGHSYGIDLKSYDLGDELGTDPIEDYEQNWNTKHGSGALRELTRELNGG 53
 
Name Accession Description Interval E-value
SARS-CoV-like_Nsp1_N cd21796
N-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related ...
 13-127 2.98e-80

N-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage; This model represents the N-terminal domain of non-structural protein 1 (Nsp1) from betacoronaviruses in the sarbecovirus subgenus (B lineage), including highly pathogenic coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). 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. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome.


Pssm-ID: 439285  Cd Length: 115  Bit Score: 233.63  E-value: 2.98e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476805  13 HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAEL 92
Cdd:cd21796     1 HVQLSLPVLQVRDVLVRGFGDSVEEALSEAREHLKNGTCGLVELEKGVLPQLEQPYVFIKRSDALSTNHGHKVVELVAEL 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1802476805  93 EGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNG 127
Cdd:cd21796    81 DGIQYGRSGITLGVLVPHVGETPIAYRNVLLRKNG 115
bCoV_NSP1 pfam11501
Betacoronavirus replicase NSP1; This entry represents the non structural protein NSP1 from ...
 9-144 8.37e-43

Betacoronavirus replicase NSP1; This entry represents the non structural protein NSP1 from Betacoronavirus NSP1 is the N-terminal cleavage product from the viral replicase that mediates RNA replication and processing. Structurally, the protein consists of a mixed parallel/antiparallel 6-stranded beta barrel with an alpha helix covering one end of the barrel and another helix alongside the barrel. NSP1 binds to the 40S ribosomal subunit and inhibits translation, and it also induces a template-dependent endonucleolytic cleavage of host mRNAs. NSP1 also suppresses the host innate immune functions by inhibiting type I interferon expression and host antiviral signalling pathways.


Pssm-ID: 431911  Cd Length: 138  Bit Score: 139.44  E-value: 8.37e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476805   9 NEKTHVQLSLPVLQVRDV-LVRGFGDSVEEVLSEARQHLK-DGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMV 86
Cdd:pfam11501   3 KRKDHVSLTLPWCDPGDVpKLTPWFMDGEEALETVKEQLKkGGKLLFVPLYLGFIKQLPGPRVYLVESLTGGWKSDPFPV 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1802476805  87 -ELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNgnkGAGGHSYGADLKSFD 144
Cdd:pfam11501  83 nELAYDDDGVRTGRSGKTVGVLFPFDPQLPTGTYTILLRKY---GLGGNSFRDVPWLWD 138
SARS-CoV-like_Nsp1_C cd22662
C-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related ...
 128-180 2.25e-32

C-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage; This model represents the C-terminal domain of non-structural protein 1 (Nsp1) from betacoronaviruses in the sarbecovirus subgenus (B lineage), including highly pathogenic coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). 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. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression. SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome. When the SARS-CoV-2 5' UTR is bound to the Nsp1 N-terminus, the covalently linked Nsp1 C-terminus cannot bind the 40S ribosome, suggesting a bipartite mechanism whereby SARS-CoV-2 Nsp1 suppresses host but not viral translation.


Pssm-ID: 439355  Cd Length: 53  Bit Score: 110.34  E-value: 2.25e-32
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1802476805 128 NKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG 180
Cdd:cd22662     1 NKGAGGHSYGIDLKSYDLGDELGTDPIEDYEQNWNTKHGSGALRELTRELNGG 53
 
Name Accession Description Interval E-value
SARS-CoV-like_Nsp1_N cd21796
N-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related ...
 13-127 2.98e-80

N-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage; This model represents the N-terminal domain of non-structural protein 1 (Nsp1) from betacoronaviruses in the sarbecovirus subgenus (B lineage), including highly pathogenic coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). 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. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome.


Pssm-ID: 439285  Cd Length: 115  Bit Score: 233.63  E-value: 2.98e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476805  13 HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAEL 92
Cdd:cd21796     1 HVQLSLPVLQVRDVLVRGFGDSVEEALSEAREHLKNGTCGLVELEKGVLPQLEQPYVFIKRSDALSTNHGHKVVELVAEL 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1802476805  93 EGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNG 127
Cdd:cd21796    81 DGIQYGRSGITLGVLVPHVGETPIAYRNVLLRKNG 115
bCoV_NSP1 pfam11501
Betacoronavirus replicase NSP1; This entry represents the non structural protein NSP1 from ...
 9-144 8.37e-43

Betacoronavirus replicase NSP1; This entry represents the non structural protein NSP1 from Betacoronavirus NSP1 is the N-terminal cleavage product from the viral replicase that mediates RNA replication and processing. Structurally, the protein consists of a mixed parallel/antiparallel 6-stranded beta barrel with an alpha helix covering one end of the barrel and another helix alongside the barrel. NSP1 binds to the 40S ribosomal subunit and inhibits translation, and it also induces a template-dependent endonucleolytic cleavage of host mRNAs. NSP1 also suppresses the host innate immune functions by inhibiting type I interferon expression and host antiviral signalling pathways.


Pssm-ID: 431911  Cd Length: 138  Bit Score: 139.44  E-value: 8.37e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476805   9 NEKTHVQLSLPVLQVRDV-LVRGFGDSVEEVLSEARQHLK-DGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMV 86
Cdd:pfam11501   3 KRKDHVSLTLPWCDPGDVpKLTPWFMDGEEALETVKEQLKkGGKLLFVPLYLGFIKQLPGPRVYLVESLTGGWKSDPFPV 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1802476805  87 -ELVAELEGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNgnkGAGGHSYGADLKSFD 144
Cdd:pfam11501  83 nELAYDDDGVRTGRSGKTVGVLFPFDPQLPTGTYTILLRKY---GLGGNSFRDVPWLWD 138
betaCoV_Nsp1 cd21876
non-structural protein 1 from betacoronavirus; This model represents the non-structural ...
 13-127 5.24e-42

non-structural protein 1 from betacoronavirus; This model represents the non-structural protein 1 (Nsp1) from betacoronaviruses, including highly pathogenic coronaviruses 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. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome.


Pssm-ID: 409338  Cd Length: 114  Bit Score: 136.77  E-value: 5.24e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476805  13 HVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDArTAPHGHVMVELVAEL 92
Cdd:cd21876     1 HVSLTLPWLQALENPVQPWIDRPEEALESAKAALAEGKLVFVPPYKGLHPLLPGPRVFLVRRHG-NPTRPFDVRELAADA 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1802476805  93 EGIQYGRSGETLGVLVPHVGEIPVAYRKVLLRKNG 127
Cdd:cd21876    80 DGVNYGRSGRTIGVLVPLDGEQPYGYINILLRKYG 114
SARS-CoV-like_Nsp1_C cd22662
C-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related ...
 128-180 2.25e-32

C-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage; This model represents the C-terminal domain of non-structural protein 1 (Nsp1) from betacoronaviruses in the sarbecovirus subgenus (B lineage), including highly pathogenic coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). 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. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression. SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome. When the SARS-CoV-2 5' UTR is bound to the Nsp1 N-terminus, the covalently linked Nsp1 C-terminus cannot bind the 40S ribosome, suggesting a bipartite mechanism whereby SARS-CoV-2 Nsp1 suppresses host but not viral translation.


Pssm-ID: 439355  Cd Length: 53  Bit Score: 110.34  E-value: 2.25e-32
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1802476805 128 NKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG 180
Cdd:cd22662     1 NKGAGGHSYGIDLKSYDLGDELGTDPIEDYEQNWNTKHGSGALRELTRELNGG 53
alpha_betaCoV_Nsp1 cd21874
non-structural protein 1 from alpha- and betacoronavirus; This model represents the ...
 13-125 8.94e-25

non-structural protein 1 from alpha- and betacoronavirus; This model represents the non-structural protein 1 (Nsp1) from alpha- and betacoronaviruses, 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. Gamma- and deltaCoVs do not have Nsp1. 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. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome.


Pssm-ID: 409336  Cd Length: 103  Bit Score: 92.27  E-value: 8.94e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476805  13 HVQLSLPVLQVrDVLVRGFGDSVEEVLSEARQHLKDG--TCGLVEVEKGVL---PQLEQPYVFIKRSDartaphghvMVE 87
Cdd:cd21874     1 SVQLSLPVLQV-DVLVRGFGDSVEEALSEAREHLKNGfgTCGFVELEKGDLvdcPQLEQYVVFVKGSK---------VVE 70

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1802476805  88 LVAELEGIqygRSGETLGVLVPHVGeiPVAYRKVLLRK 125
Cdd:cd21874    71 LVAEMDGI---RSGITLGVLVPHNC--NIALENVLLRK 103
HKU9-like_Nsp1 cd21877
non-structural protein 1 from Rousettus bat coronavirus HKU9 and betacoronavirus in the D ...
 28-160 3.57e-06

non-structural protein 1 from Rousettus bat coronavirus HKU9 and betacoronavirus in the D lineage; This model represents the non-structural protein 1 (Nsp1) from betacoronavirus in the nobecovirus subgenus (D lineage), including Rousettus bat coronavirus HKU9. 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. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome.


Pssm-ID: 409339  Cd Length: 165  Bit Score: 44.71  E-value: 3.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476805  28 VRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVL--PQLEQPYVFIKRSDARTAPHGHVMV-ELVAELEGIQYGRSGeTL 104
Cdd:cd21877    22 VTGWDMPIEEALEYVKRELRKPEPQLVFVPNYLChsPLIGRDRVVITDSIWRATEMGWQPIrELAFDKDGVRYGRGG-TY 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1802476805 105 GVLVPH------VGEIPVAYRKVllrkngnkGAGGHSYGADLKSFD--LGDELGTDPYEDFQEN 160
Cdd:cd21877   101 GVLLPMqdsqyiMGTVDIDIRKY--------GVGAGSDPDVPPLWDgfVDPPIPEDDYLDFPDN 156
MHV-like_Nsp1 cd21879
non-structural protein 1 from murine hepatitis virus and betacoronavirus in the A lineage; ...
 13-167 5.29e-05

non-structural protein 1 from murine hepatitis virus and betacoronavirus in the A lineage; This model represents the non-structural protein 1 (Nsp1) from betacoronavirus in the embecovirus subgenus (A lineage), including murine hepatitis virus (MHV), bovine coronavirus (BCoV) and Human coronavirus HKU1. 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. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and MHV genomes cause drastic reduction or elimination of infectious virus; BCoV Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome.


Pssm-ID: 409341  Cd Length: 236  Bit Score: 42.37  E-value: 5.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476805  13 HVQLSLpvlqVRDVLVRGFGDSVEEVLSEArqhLKDGTCGLVE----------VEKGVLPQLEQPYVFIKRSDART---A 79
Cdd:cd21879    66 CVQSNL----IRDIFVDTDPYDVEVLTQDA---LQSGEAVLVKpplrmsleacYKLGCLPKGWAMGLFRRRCVCNTgrcG 138

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1802476805  80 PHGHVMVEL-VAELEGIQYGrSGETLGVLVPhVGEIPVAYRK------VLLRKNGNKGA--GGHSYGADLKSFDLGDElg 150
Cdd:cd21879   139 VDKHVAYQLfMIDPDGVCLG-AGRFIGWVVP-LAFIPEYARKwlqpwvIYLRKYGEKGAytKGHKRGGFGHVYDFKVE-- 214

                         170
                  ....*....|....*..
gi 1802476805 151 tDPYEDFQENWNTKHSS 167
Cdd:cd21879   215 -DAYDEVHDEPKGKYSK 230
 
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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