ORF1ab ORF1a polyprotein;ORF1ab polyprotein [Severe acute respiratory syndrome coronavirus 2] - Gene

Summary

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Gene symbol: ORF1ab
Gene description: ORF1a polyprotein;ORF1ab polyprotein
Locus tag: GU280_gp01
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Severe acute respiratory syndrome coronavirus 2 (isolate: Wuhan-Hu-1, nat-host: Homo sapiens)
Lineage: Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae; Betacoronavirus; Sarbecovirus
Summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped, positive-sense, single-stranded RNA virus that causes coronavirus disease 2019 (COVID-19). Virus particles include the RNA genetic material and structural proteins needed for invasion of host cells. Once inside the cell the infecting RNA is used to encode structural proteins that make up virus particles, nonstructural proteins that direct virus assembly, transcription, replication and host control and accessory proteins whose function has not been determined.~ ORF1ab, the largest gene, contains overlapping open reading frames that encode polyproteins PP1ab and PP1a. The polyproteins are cleaved to yield 16 nonstructural proteins, NSP1-16. Production of the longer (PP1ab) or shorter protein (PP1a) depends on a -1 ribosomal frameshifting event. The proteins, based on similarity to other coronaviruses, include the papain-like proteinase protein (NSP3), 3C-like proteinase (NSP5), RNA-dependent RNA polymerase (NSP12, RdRp), helicase (NSP13, HEL), endoRNAse (NSP15), 2'-O-Ribose-Methyltransferase (NSP16) and other nonstructural proteins. SARS-CoV-2 nonstructural proteins are responsible for viral transcription, replication, proteolytic processing, suppression of host immune responses and suppression of host gene expression. The RNA-dependent RNA polymerase is a target of antiviral therapies.
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Genomic context

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Sequence:: NC_045512.2 (266..21555)

NC_045512.2 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:: NC_045512.2

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nsp1 facilitates SARS-CoV-2 replication through calcineurin-NFAT signaling.
Title: Nsp1 facilitates SARS-CoV-2 replication through calcineurin-NFAT signaling.
Structural Basis for the Inhibition of SARS-CoV-2 M[pro] D48N Mutant by Shikonin and PF-07321332.
Title: Structural Basis for the Inhibition of SARS-CoV-2 M(pro) D48N Mutant by Shikonin and PF-07321332.
Epigenetic repression of antiviral genes by SARS-CoV-2 NSP1.
Title: Epigenetic repression of antiviral genes by SARS-CoV-2 NSP1.
E3 ubiquitin ligase ZBTB25 suppresses beta coronavirus infection through ubiquitination of the main viral protease MPro.
Title: E3 ubiquitin ligase ZBTB25 suppresses beta coronavirus infection through ubiquitination of the main viral protease MPro.
Three distinct ORF1a recombinants of the SARS-CoV-2 Delta variant of concern.
Title: Three distinct ORF1a recombinants of the SARS-CoV-2 Delta variant of concern.
Improved expression and purification of highly-active 3 chymotrypsin-like protease from SARS-CoV-2.
Title: Improved expression and purification of highly-active 3 chymotrypsin-like protease from SARS-CoV-2.
Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16.
Title: Emerging variants of SARS-CoV-2 NSP10 highlight strong functional conservation of its binding to two non-structural proteins, NSP14 and NSP16.
SARS-CoV-2 Nsp8 suppresses MDA5 antiviral immune responses by impairing TRIM4-mediated K63-linked polyubiquitination.
Title: SARS-CoV-2 Nsp8 suppresses MDA5 antiviral immune responses by impairing TRIM4-mediated K63-linked polyubiquitination.
RNA-dependent RNA polymerase of SARS-CoV-2 regulate host mRNA translation efficiency by hijacking eEF1A factors.
Title: RNA-dependent RNA polymerase of SARS-CoV-2 regulate host mRNA translation efficiency by hijacking eEF1A factors.
SARS-COV-2 protein NSP9 promotes cytokine production by targeting TBK1.
Title: SARS-COV-2 protein NSP9 promotes cytokine production by targeting TBK1.

Submit: New GeneRIF Correction See all GeneRIFs (141)

Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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stem_loop

Loc: 13476-13503 function = Coronavirus frameshifting stimulation element stem-loop 1 , inference = COORDINATES: profile:Rfam-release-14.1:RF00507,Infernal:1.1.2
Loc: 13488-13542 function = Coronavirus frameshifting stimulation element stem-loop 2 , inference = COORDINATES: profile:Rfam-release-14.1:RF00507,Infernal:1.1.2

General protein information

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Preferred Names: ORF1a polyprotein;ORF1ab polyprotein

Names: leader protein; nsp2; nsp3; nsp4; 3C-like proteinase; nsp6; nsp7; nsp8; nsp9; nsp10; RNA-dependent RNA polymerase; helicase; 3'-to-5' exonuclease; endoRNAse; 2'-O-ribose methyltransferase; leader protein; nsp2; nsp3; nsp4; 3C-like proteinase; nsp6; nsp7; nsp8; nsp9; nsp10; nsp11

YP_009724389.1

pp1ab; translated by -1 ribosomal frameshift

YP_009725295.1

pp1a

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_045512.2 Reference assembly

Range

266..21555

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

YP_009724389.1 ORF1ab polyprotein [Severe acute respiratory syndrome coronavirus 2]

Status: PROVISIONAL

UniProtKB/Swiss-Prot

P0DTD1

UniProtKB/TrEMBL

A0A679G4D8, A0A6B9UY63, A0A6B9V049, A0A6B9VSU5, A0A6B9WIH5, A0A6C0M7K8, A0A6C0RS15, A0A6C0T6V0, A0A6C1F1G5, A0A6G7CR93, A0A6H2L6K3, A0A6H2TXR8, A0A6M3DDN3, A0A6M3GZB3, A0A6M3HQ10, A0A6M3HT58, A0A6M3T1R2, A0A6M5WPR7, A0A6M8EHB3, A0A6N1W2H4, A0A6V7AKV6, A0A6V7ALW7, A0A7I0YLY4, A0A7U3MRI0, A0A7U3MX55, A0A7U3RLH4, A0A883GPD4, A0A886NG00

Conserved Domains (29) summary

pfam11633
Location:1351 → 1493

SUD-M; Single-stranded poly(A) binding domain

cd21401
Location:5325 → 5419

ZBD_cv_Nsp13-like; Cys/His rich zinc-binding domain (CH/ZBD) of coronavirus SARS NSP13 helicase and related proteins

cd21409
Location:5474 → 5552

1B_cv_Nsp13-like; 1B domain of coronavirus SARS NSP13 helicase and related proteins

cd21473
Location:2777 → 3157

cv_Nsp4_TM; coronavirus non-structural protein 4 (Nsp4) transmembrane domain

cd21525
Location:1496 → 1561

SUD_C_SARS-CoV_Nsp3; C-terminal SARS-Unique Domain (SUD) of non-structural protein 3 (Nsp3) from Severe Acute Respiratory Syndrome coronavirus and related betacoronaviruses in the B lineage

cd21560
Location:3570 → 3859

betaCoV-Nsp6; betacoronavirus non-structural protein 6

cd21516
Location:182 → 818

cv_beta_Nsp2_SARS-like; betacoronavirus non-structural protein 2 (Nsp2) similar to SARS-CoV Nsp2, and related proteins from betacoronaviruses in the B lineage

cd21557
Location:1054 → 1177

Macro_X_Nsp3-like; X-domain of viral non-structural protein 3 and related macrodomains

cd21666
Location:3267 → 3563

betaCoV_Nsp5_Mpro; betacoronavirus non-structural protein 5, also called Main protease (Mpro)

cd21591
Location:4397 → 5324

SARS-CoV-like_RdRp; Severe acute respiratory syndrome coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the B lineage: responsible for replication and transcription of the viral RNA genome

cd21171
Location:6453 → 6513

NTD_alpha_beta_cv_Nsp15-like; N-terminal domain of alpha- and beta-coronavirus Nonstructural protein 15 (Nsp15), and related proteins

cd21167
Location:6517 → 6648

M_alpha_beta_cv_Nsp15-like; middle domain of alpha- and beta-coronavirus Nonstructural protein 15 (Nsp15), and related proteins

cd21161
Location:6646 → 6796

NendoU_cv_Nsp15-like; Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural Protein 15 (Nsp15) and related proteins

cd21659
Location:5930 → 6450

betaCoV_Nsp14; nonstructural protein 14 of betacoronavirus

pfam06460
Location:6800 → 7095

NSP13; Coronavirus NSP13

pfam08717
Location:3943 → 4139

nsp8; nsp8 replicase

pfam12379
Location:880 → 1050

DUF3655; Protein of unknown function (DUF3655)

pfam16348
Location:3169 → 3261

Corona_NSP4_C; Coronavirus nonstructural protein 4 C-terminus

cd21827
Location:3860 → 3942

betaCoV_Nsp7; betacoronavirus non-structural protein 7

cd21901
Location:4254 → 4384

alpha_betaCoV_Nsp10; alphacoronavirus and betacoronavirus non-structural protein 14

cd21898
Location:4141 → 4253

betaCoV_Nsp9; betacoronavirus non-structural protein 9

cd21796
Location:13 → 127

SARS-CoV-like_Nsp1_N; N-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage

cd21822
Location:1913 → 2019

SARS-CoV-like_Nsp3_NAB; nucleic acid binding domain of non-structural protein 3 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage

cd21814
Location:2044 → 2159

SARS-CoV-like_Nsp3_betaSM; betacoronavirus-specific marker of non-structural protein 3 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage

cd21732
Location:1566 → 1868

betaCoV_PLPro; betacoronavirus papain-like protease

cd21722
Location:5575 → 5914

betaCoV_Nsp13-helicase; helicase domain of betacoronavirus non-structural protein 13

cd21717
Location:2232 → 2762

TM_Y_SARS-CoV-like_Nsp3_C; C-terminus of non-structural protein 3, including transmembrane and Y domains, from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage

cd21689
Location:5423 → 5470

stalk_CoV_Nsp13-like; stalk domain of coronavirus Nsp13 helicase and related proteins

cl00019
Location:1233 → 1358

Macro_SF; macrodomain superfamily
YP_009725297.1 leader protein

UniProtKB/TrEMBL

A0A6M8NMS9, A0A6M8NRD9

Conserved Domains (1) summary

cl41742
Location:13 → 127

alpha_betaCoV_Nsp1; non-structural protein 1 from alpha- and betacoronavirus
YP_009725298.1 nsp2

Conserved Domains (1) summary

cd21516
Location:2 → 638

cv_beta_Nsp2_SARS-like; betacoronavirus non-structural protein 2 (Nsp2) similar to SARS-CoV Nsp2, and related proteins from betacoronaviruses in the B lineage
YP_009725299.1 nsp3

Conserved Domains (8) summary

pfam12124
Location:680 → 743

Nsp3_PL2pro; Coronavirus polyprotein cleavage domain

pfam12379
Location:102 → 169

DUF3655; Protein of unknown function (DUF3655)

pfam16251
Location:1089 → 1201

NAR; Nucleic acid-binding domain (NAR)

pfam11633
Location:533 → 675

SUD-M; Single-stranded poly(A) binding domain

cd14964
Location:1497 → 1519

7tm_GPCRs; TM helix 5 [structural motif]

pfam01661
Location:240 → 340

Macro; Macro domain

pfam08715
Location:746 → 1064

Viral_protease; Papain like viral protease

cl28897
Location:1494 → 1563

7tm_GPCRs; seven-transmembrane G protein-coupled receptor superfamily
YP_009725300.1 nsp4

Conserved Domains (1) summary

pfam16348
Location:406 → 498

Corona_NSP4_C; Coronavirus nonstructural protein 4 C-terminus
YP_009725301.1 3C-like proteinase

Conserved Domains (1) summary

cd21666
Location:4 → 300

betaCoV_Nsp5_Mpro; betacoronavirus non-structural protein 5, also called Main protease (Mpro)
YP_009725302.1 nsp6
YP_009725303.1 nsp7

Conserved Domains (1) summary

cd21827
Location:1 → 83

betaCoV_Nsp7; betacoronavirus non-structural protein 7
YP_009725304.1 nsp8

Conserved Domains (1) summary

pfam08717
Location:1 → 197

nsp8; nsp8 replicase
YP_009725305.1 nsp9

Conserved Domains (1) summary

cd21898
Location:1 → 113

betaCoV_Nsp9; betacoronavirus non-structural protein 9
YP_009725306.1 nsp10

UniProtKB/TrEMBL

G8H303

Conserved Domains (1) summary

cl40460
Location:1 → 131

CoV_Nsp10; coronavirus non-structural protein 10
YP_009725307.1 RNA-dependent RNA polymerase

Conserved Domains (1) summary

cd21591
Location:5 → 932

SARS-CoV-like_RdRp; Severe acute respiratory syndrome coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the B lineage: responsible for replication and transcription of the viral RNA genome
YP_009725308.1 helicase

Conserved Domains (4) summary

cd21401
Location:1 → 95

ZBD_cv_Nsp13-like; Cys/His rich zinc-binding domain (CH/ZBD) of coronavirus SARS NSP13 helicase and related proteins

cd21409
Location:150 → 228

1B_cv_Nsp13-like; 1B domain of coronavirus SARS NSP13 helicase and related proteins

cd21722
Location:251 → 590

betaCoV_Nsp13-helicase; helicase domain of betacoronavirus non-structural protein 13

cd21689
Location:99 → 146

stalk_CoV_Nsp13-like; stalk domain of coronavirus Nsp13 helicase and related proteins
YP_009725309.1 3'-to-5' exonuclease

Conserved Domains (1) summary

cl40464
Location:5 → 525

CoV_Nsp14; nonstructural protein 14 of coronavirus
YP_009725310.1 endoRNAse

Conserved Domains (1) summary

pfam06471
Location:1 → 68

NSP11
YP_009725311.1 2'-O-ribose methyltransferase

Conserved Domains (1) summary

pfam06460
Location:2 → 297

NSP13; Coronavirus NSP13
YP_009725295.1 ORF1a polyprotein [Severe acute respiratory syndrome coronavirus 2]

Status: PROVISIONAL

UniProtKB/Swiss-Prot

P0DTC1

UniProtKB/TrEMBL

A0A6C0RSH1, A0A6G6A224, A0A6G7KRG6, A0A6H0C7F2, A0A6H0JG04, A0A6M3HSG4, A0A6M3VXV6, A0A6M3WSK0, A0A6M5WJ06, A0A6M5WNZ9, A0A6M6JVJ9, A0A7D5JHC2, A0A7G6WCV0, A0A7G9UIU5, A0A7H4JDL9, A0A7T4X8V7, A0A7U1D8T7, A0A7U3HE26, A0A7U3QAS2, A0A883GPP4, A0A883GQI3, A0A883GR30, A0A897FAK2, A0A897FEG2, A0A8B1JJQ7, A0A8B1JX69, A0A8B6RCQ2

Conserved Domains (19) summary

pfam11633
Location:1351 → 1493

SUD-M; Single-stranded poly(A) binding domain

cd21473
Location:2777 → 3157

cv_Nsp4_TM; coronavirus non-structural protein 4 (Nsp4) transmembrane domain

cd21525
Location:1496 → 1561

SUD_C_SARS-CoV_Nsp3; C-terminal SARS-Unique Domain (SUD) of non-structural protein 3 (Nsp3) from Severe Acute Respiratory Syndrome coronavirus and related betacoronaviruses in the B lineage

cd21560
Location:3570 → 3859

betaCoV-Nsp6; betacoronavirus non-structural protein 6

cd21516
Location:182 → 818

cv_beta_Nsp2_SARS-like; betacoronavirus non-structural protein 2 (Nsp2) similar to SARS-CoV Nsp2, and related proteins from betacoronaviruses in the B lineage

cd21557
Location:1054 → 1177

Macro_X_Nsp3-like; X-domain of viral non-structural protein 3 and related macrodomains

cd21666
Location:3267 → 3563

betaCoV_Nsp5_Mpro; betacoronavirus non-structural protein 5, also called Main protease (Mpro)

pfam08717
Location:3943 → 4139

nsp8; nsp8 replicase

pfam12379
Location:880 → 1050

DUF3655; Protein of unknown function (DUF3655)

pfam16348
Location:3169 → 3261

Corona_NSP4_C; Coronavirus nonstructural protein 4 C-terminus

cd21827
Location:3860 → 3942

betaCoV_Nsp7; betacoronavirus non-structural protein 7

cd21901
Location:4254 → 4384

alpha_betaCoV_Nsp10; alphacoronavirus and betacoronavirus non-structural protein 14

cd21898
Location:4141 → 4253

betaCoV_Nsp9; betacoronavirus non-structural protein 9

cd21796
Location:13 → 127

SARS-CoV-like_Nsp1_N; N-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage

cd21822
Location:1913 → 2019

SARS-CoV-like_Nsp3_NAB; nucleic acid binding domain of non-structural protein 3 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage

cd21732
Location:1566 → 1868

betaCoV_PLPro; betacoronavirus papain-like protease

cd21717
Location:2232 → 2762

TM_Y_SARS-CoV-like_Nsp3_C; C-terminus of non-structural protein 3, including transmembrane and Y domains, from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage

cl00019
Location:1233 → 1358

Macro_SF; macrodomain superfamily

cl41743
Location:2044 → 2159

betaCoV_Nsp3_betaSM; betacoronavirus-specific marker of betacoronavirus non-structural protein 3
YP_009742608.1 leader protein

UniProtKB/TrEMBL

A0A6M8NMS9, A0A6M8NRD9

Conserved Domains (1) summary

cl41742
Location:13 → 127

alpha_betaCoV_Nsp1; non-structural protein 1 from alpha- and betacoronavirus
YP_009742609.1 nsp2

Conserved Domains (1) summary

cd21516
Location:2 → 638

cv_beta_Nsp2_SARS-like; betacoronavirus non-structural protein 2 (Nsp2) similar to SARS-CoV Nsp2, and related proteins from betacoronaviruses in the B lineage
YP_009742610.1 nsp3

Conserved Domains (8) summary

pfam12124
Location:680 → 743

Nsp3_PL2pro; Coronavirus polyprotein cleavage domain

pfam12379
Location:102 → 169

DUF3655; Protein of unknown function (DUF3655)

pfam16251
Location:1089 → 1201

NAR; Nucleic acid-binding domain (NAR)

pfam11633
Location:533 → 675

SUD-M; Single-stranded poly(A) binding domain

cd14964
Location:1497 → 1519

7tm_GPCRs; TM helix 5 [structural motif]

pfam01661
Location:240 → 340

Macro; Macro domain

pfam08715
Location:746 → 1064

Viral_protease; Papain like viral protease

cl28897
Location:1494 → 1563

7tm_GPCRs; seven-transmembrane G protein-coupled receptor superfamily
YP_009742611.1 nsp4

Conserved Domains (1) summary

pfam16348
Location:406 → 498

Corona_NSP4_C; Coronavirus nonstructural protein 4 C-terminus
YP_009742612.1 3C-like proteinase

Conserved Domains (1) summary

cd21666
Location:4 → 300

betaCoV_Nsp5_Mpro; betacoronavirus non-structural protein 5, also called Main protease (Mpro)
YP_009742613.1 nsp6
YP_009742614.1 nsp7

Conserved Domains (1) summary

cd21827
Location:1 → 83

betaCoV_Nsp7; betacoronavirus non-structural protein 7
YP_009742615.1 nsp8

Conserved Domains (1) summary

pfam08717
Location:1 → 197

nsp8; nsp8 replicase
YP_009742616.1 nsp9

Conserved Domains (1) summary

cd21898
Location:1 → 113

betaCoV_Nsp9; betacoronavirus non-structural protein 9
YP_009742617.1 nsp10

UniProtKB/TrEMBL

G8H303

Conserved Domains (1) summary

cl40460
Location:1 → 131

CoV_Nsp10; coronavirus non-structural protein 10
YP_009725312.1 nsp11