ORF1ab ORF1a polyprotein;ORF1ab polyprotein [SARS coronavirus Tor2] - Gene

Summary

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Gene symbol: ORF1ab
Gene description: ORF1a polyprotein;ORF1ab polyprotein
Locus tag: sarsp1
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: SARS coronavirus Tor2 (isolate: Tor2, nat-host: Homo sapiens; patient #2 with severe acute respiratory syndrome (SARS))
Lineage: Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes; Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae; Betacoronavirus; Sarbecovirus
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Genomic context

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Sequence:: NC_004718.3 (265..21485)

NC_004718.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_004718.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Molecular and Structural Analysis of Specific Mutations from Saudi Isolates of SARS-CoV-2 RNA-Dependent RNA Polymerase and their Implications on Protein Structure and Drug-Protein Binding.
Title: Molecular and Structural Analysis of Specific Mutations from Saudi Isolates of SARS-CoV-2 RNA-Dependent RNA Polymerase and their Implications on Protein Structure and Drug-Protein Binding.
Structural Basis and Function of the N Terminus of SARS-CoV-2 Nonstructural Protein 1.
Title: Structural Basis and Function of the N Terminus of SARS-CoV-2 Nonstructural Protein 1.
Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response.
Title: Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response.
Data indicate cellular E3 ubiquitin ligase ring-finger and CHY zinc-finger domain-containing 1 (RCHY1) as an interacting partner of the viral SARS-unique domain (SUD) and papain-like protease (PL(pro)), and, as a consequence, the involvement of cellular p53 as antagonist of coronaviral replication.
Title: p53 down-regulates SARS coronavirus replication and is targeted by the SARS-unique domain and PLpro via E3 ubiquitin ligase RCHY1.
Finally, the authors showed that loss of the nsp3-nsp4 interaction eliminated viral replication by using an infectious cDNA clone and replicon system of SARS coronavirus.
Title: Two-amino acids change in the nsp4 of SARS coronavirus abolishes viral replication.
Report specificity of Lys48-linked di-ubiquitin and deubiquitinating activities of the SARS coronavirus papain-like protease.
Title: Recognition of Lys48-Linked Di-ubiquitin and Deubiquitinating Activities of the SARS Coronavirus Papain-like Protease.
While the SUD-N and the X domains were found to be dispensable, the SUD-M domain of nsp3 protein was crucial for viral genome replication/transcription.
Title: A G-quadruplex-binding macrodomain within the "SARS-unique domain" is essential for the activity of the SARS-coronavirus replication-transcription complex.
analysis of the architecture of the nsp14-nsp10 complex involved in RNA viral proofreading
Title: Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex.
The data show that SARS coronavirus PLpro also inhibits IRF3 activation at a step after phosphorylation and that this inhibition is dependent on the de-ubiquitination (DUB) activity of PLpro.
Title: The SARS coronavirus papain like protease can inhibit IRF3 at a post activation step that requires deubiquitination activity.
identification of sites in PLpro required for recognition and processing of diubiquitin and ISG15 provides insight into ubiquitin-chain and ISG15 recognition and highlights role for PLpro DUB and deISGylase activity in antagonism of innate immune response
Title: Structural Basis for the Ubiquitin-Linkage Specificity and deISGylating activity of SARS-CoV papain-like protease.

Submit: New GeneRIF Correction See all GeneRIFs (23)

Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General protein information

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Preferred Names: ORF1a polyprotein;ORF1ab polyprotein

Names: polyprotein pp1a; polyprotein pp1ab; replicase 1AB; nsp1; nsp2; nsp3; nsp4; 3C-like protease; nsp6; nsp7; nsp8; nsp9; nsp10; RNA-dependent RNA polymerase; helicase/NTPase; endoribonuclease; 2'-O-MTase; 3' to 5' exonuclease; nsp1; nsp2; nsp3; nsp4; 3C-like protease; nsp6; nsp7; nsp8; nsp9; nsp10; ndp11

NP_828849.7

ORF1ab polyprotein is cleaved to yield the RNA-dependent RNA polymerase and other nonstructural proteins

YP_009944365.1

ORF1a polyprotein is cleaved to yield nonstructural proteins

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_004718.3 Reference assembly

Range

265..21485

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NP_828849.7 ORF1ab polyprotein [SARS coronavirus Tor2]

Status: PROVISIONAL

UniProtKB/Swiss-Prot

P0C6X7, P59641, Q6WGN0, Q7T697, Q808C0, Q80BV7, Q80BV8, Q80E51

UniProtKB/TrEMBL

A7J8L2, B8Q8Q1, C4P6Q5, D3KDM3, J9T571, Q5Y189, Q6RCY9, Q6RD00, Q6RD11, Q6RD44, Q6RD66, Q6UZF5, Q6VA91, Q6VAA2

Conserved Domains (29) summary

pfam11633
Location:1327 → 1469

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

cd21401
Location:5302 → 5396

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

cd21409
Location:5451 → 5529

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

cd21473
Location:2754 → 3134

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

cd21525
Location:1472 → 1538

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:3547 → 3836

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:1034 → 1155

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

cd21562
Location:1209 → 1334

Macro_cv_SUD-N_Nsp3-like; SUD-N macrodomain of the SARS Unique Domain (SUD) of SARS-CoV non-structural protein 3 and related macrodomains

cd21666
Location:3244 → 3540

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

cd21591
Location:4375 → 5301

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:6430 → 6490

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

cd21167
Location:6494 → 6625

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

cd21161
Location:6623 → 6773

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

cd21659
Location:5907 → 6427

betaCoV_Nsp14; nonstructural protein 14 of betacoronavirus

pfam06460
Location:6777 → 7072

NSP13; Coronavirus NSP13

pfam08717
Location:3920 → 4116

nsp8; nsp8 replicase

pfam12379
Location:881 → 1029

DUF3655; Protein of unknown function (DUF3655)

pfam16348
Location:3146 → 3238

Corona_NSP4_C; Coronavirus nonstructural protein 4 C-terminus

cd21827
Location:3837 → 3919

betaCoV_Nsp7; betacoronavirus non-structural protein 7

cd21872
Location:4231 → 4361

CoV_Nsp10; coronavirus non-structural protein 10

cd21898
Location:4118 → 4230

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:1890 → 1996

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:2021 → 2136

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:1543 → 1845

betaCoV_PLPro; betacoronavirus papain-like protease

cd21722
Location:5552 → 5891

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

cd21717
Location:2209 → 2739

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:5400 → 5447

stalk_CoV_Nsp13-like; stalk domain of coronavirus Nsp13 helicase and related proteins
NP_828860.2 nsp1

Conserved Domains (1) summary

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
NP_828861.2 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
NP_828862.2 nsp3

Conserved Domains (9) summary

pfam11633
Location:509 → 651

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

cd21525
Location:654 → 720

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

cd21557
Location:214 → 337

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

cd21562
Location:391 → 516

Macro_cv_SUD-N_Nsp3-like; SUD-N macrodomain of the SARS Unique Domain (SUD) of SARS-CoV non-structural protein 3 and related macrodomains

pfam12379
Location:63 → 211

DUF3655; Protein of unknown function (DUF3655)

cd21822
Location:1072 → 1178

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:1203 → 1318

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:725 → 1027

betaCoV_PLPro; betacoronavirus papain-like protease

cd21717
Location:1391 → 1921

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
NP_904322.1 nsp4

Conserved Domains (2) summary

cd21473
Location:14 → 394

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

pfam16348
Location:406 → 498

Corona_NSP4_C; Coronavirus nonstructural protein 4 C-terminus
NP_828863.1 3C-like protease

UniProtKB/TrEMBL

G8H301

Conserved Domains (1) summary

cd21666
Location:4 → 300

betaCoV_Nsp5_Mpro; betacoronavirus non-structural protein 5, also called Main protease (Mpro)
NP_828864.1 nsp6

Conserved Domains (1) summary

cd21560
Location:1 → 290

betaCoV-Nsp6; betacoronavirus non-structural protein 6
NP_828865.1 nsp7

Conserved Domains (1) summary

cd21827
Location:1 → 83

betaCoV_Nsp7; betacoronavirus non-structural protein 7
NP_828866.1 nsp8

Conserved Domains (1) summary

pfam08717
Location:1 → 197

nsp8; nsp8 replicase
NP_828867.1 nsp9

Conserved Domains (1) summary

cd21898
Location:1 → 113

betaCoV_Nsp9; betacoronavirus non-structural protein 9
NP_828868.1 nsp10

UniProtKB/TrEMBL

G8H302, G8H303

Conserved Domains (1) summary

cd21901
Location:1 → 131

alpha_betaCoV_Nsp10; alphacoronavirus and betacoronavirus non-structural protein 14
YP_009924301.1 RNA-dependent RNA polymerase
NP_828870.1 helicase/NTPase

Conserved Domains (3) summary

COG1112
Location:323 → 592

DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]

cl21455
Location:277 → 407

P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

cl22977
Location:443 → 580

UvrD_C_2; UvrD-like helicase C-terminal domain
NP_828872.1 endoribonuclease

Conserved Domains (3) summary

cd21171
Location:1 → 61

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

cd21167
Location:65 → 196

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

cd21161
Location:194 → 344

NendoU_cv_Nsp15-like; Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural Protein 15 (Nsp15) and related proteins
NP_828873.2 2'-O-MTase

UniProtKB/TrEMBL

G8H306

Conserved Domains (1) summary

pfam06460
Location:2 → 297

NSP13; Coronavirus NSP13
NP_828871.1 3' to 5' exonuclease

Conserved Domains (1) summary

cd21659
Location:5 → 525

betaCoV_Nsp14; nonstructural protein 14 of betacoronavirus
YP_009944365.1 ORF1a polyprotein [SARS coronavirus Tor2]

Status: PROVISIONAL

UniProtKB/Swiss-Prot

P0C6U8

UniProtKB/TrEMBL

A0A3G5BIY1, A7J8L3, B8Q8Q2, C4P6Q6, D2E1D1, D3KDM4, D3KDQ2, H9CHT9, J9SE37, J9T0Q3, J9TCC0, Q1EFN3, Q1EFP6, Q5Y188, Q6JH39, Q6JH47, Q6RCW6, Q6RCX7, Q6RCY8, Q6RCZ9, Q6RD10, Q6RD21, Q6RD32, Q6RD43, Q6RD65, Q6VA79, Q6VA90, Q6VAA1

Conserved Domains (19) summary

pfam11633
Location:1327 → 1469

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

cd21473
Location:2754 → 3134

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

cd21525
Location:1472 → 1538

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:3547 → 3836

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:1034 → 1155

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

cd21562
Location:1209 → 1334

Macro_cv_SUD-N_Nsp3-like; SUD-N macrodomain of the SARS Unique Domain (SUD) of SARS-CoV non-structural protein 3 and related macrodomains

cd21666
Location:3244 → 3540

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

pfam08717
Location:3920 → 4116

nsp8; nsp8 replicase

pfam12379
Location:881 → 1029

DUF3655; Protein of unknown function (DUF3655)

pfam16348
Location:3146 → 3238

Corona_NSP4_C; Coronavirus nonstructural protein 4 C-terminus

cd21827
Location:3837 → 3919

betaCoV_Nsp7; betacoronavirus non-structural protein 7

cd21872
Location:4231 → 4361

CoV_Nsp10; coronavirus non-structural protein 10

cd21898
Location:4118 → 4230

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:1890 → 1996

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:2021 → 2136

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:1543 → 1845

betaCoV_PLPro; betacoronavirus papain-like protease

cd21717
Location:2209 → 2739

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
YP_009944366.1 nsp1

Conserved Domains (1) summary

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
YP_009944367.1 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_009944368.1 nsp3

Conserved Domains (9) summary

pfam11633
Location:509 → 651

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

cd21525
Location:654 → 720

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

cd21557
Location:214 → 337

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

cd21562
Location:391 → 516

Macro_cv_SUD-N_Nsp3-like; SUD-N macrodomain of the SARS Unique Domain (SUD) of SARS-CoV non-structural protein 3 and related macrodomains

pfam12379
Location:63 → 211

DUF3655; Protein of unknown function (DUF3655)

cd21822
Location:1072 → 1178

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:1203 → 1318

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:725 → 1027

betaCoV_PLPro; betacoronavirus papain-like protease

cd21717
Location:1391 → 1921

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
YP_009944369.1 nsp4

Conserved Domains (2) summary

cd21473
Location:14 → 394

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

pfam16348
Location:406 → 498

Corona_NSP4_C; Coronavirus nonstructural protein 4 C-terminus
YP_009944370.1 3C-like protease

UniProtKB/TrEMBL

G8H301

Conserved Domains (1) summary

cd21666
Location:4 → 300

betaCoV_Nsp5_Mpro; betacoronavirus non-structural protein 5, also called Main protease (Mpro)
YP_009944371.1 nsp6

Conserved Domains (1) summary

cd21560
Location:1 → 290

betaCoV-Nsp6; betacoronavirus non-structural protein 6
YP_009944372.1 nsp7

Conserved Domains (1) summary

cd21827
Location:1 → 83

betaCoV_Nsp7; betacoronavirus non-structural protein 7
YP_009944373.1 nsp8

Conserved Domains (1) summary

pfam08717
Location:1 → 197

nsp8; nsp8 replicase
YP_009944374.1 nsp9

Conserved Domains (1) summary

cd21898
Location:1 → 113

betaCoV_Nsp9; betacoronavirus non-structural protein 9
YP_009944375.1 nsp10

UniProtKB/TrEMBL

G8H302, G8H303

Conserved Domains (1) summary

cd21901
Location:1 → 131

alpha_betaCoV_Nsp10; alphacoronavirus and betacoronavirus non-structural protein 14
YP_009944376.1 ndp11