rep

Functionⁱ

The replicase polyprotein of coronaviruses is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products.

By similarity

Host translation inhibitor nsp1:

Inhibits host translation by interacting with the 40S ribosomal subunit. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. Viral mRNAs are not susceptible to nsp1-mediated endonucleolytic RNA cleavage thanks to the presence of a 5'-end leader sequence and are therefore protected from degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response.

By similarity

Non-structural protein 2:

May play a role in the modulation of host cell survival signaling pathway by interacting with host PHB and PHB2. Indeed, these two proteins play a role in maintaining the functional integrity of the mitochondria and protecting cells from various stresses.

By similarity

Papain-like proteinase:

Responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3. Prevents also host NF-kappa-B signaling.

By similarity

Non-structural protein 4:

Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.

By similarity

3C-like proteinase:

Cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Also able to bind an ADP-ribose-1''-phosphate (ADRP).

PROSITE-ProRule annotationBy similarity

Non-structural protein 6:

Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic. Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes.

By similarity

Non-structural protein 7:

Forms a hexadecamer with nsp8 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.

By similarity

Non-structural protein 8:

Forms a hexadecamer with nsp7 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.

By similarity

Non-structural protein 9:

May participate in viral replication by acting as a ssRNA-binding protein.

By similarity

Non-structural protein 10:

Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease and nsp16 2'-O-methyltransferase activities. Therefore plays an essential role in viral mRNAs cap methylation.

By similarity

RNA-directed RNA polymerase:

Responsible for replication and transcription of the viral RNA genome.

By similarity

Helicase:

Multi-functional protein with a zinc-binding domain in N-terminus displaying RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Activity of helicase is dependent on magnesium.

By similarity

Guanine-N7 methyltransferase:

Enzyme possessing two different activities: an exoribonuclease activity acting on both ssRNA and dsRNA in a 3' to 5' direction and a N7-guanine methyltransferase activity.

By similarity

Uridylate-specific endoribonuclease:

Plays a role in viral transcription/replication and prevents the simultaneous activation of host cell dsRNA sensors, such as MDA5/IFIH1, OAS, and PKR (By similarity).

Acts by degrading the 5'-polyuridines generated during replication of the poly(A) region of viral genomic and subgenomic RNAs. Catalyzes a two-step reaction in which a 2'3'-cyclic phosphate (2'3'-cP) is first generated by 2'-O transesterification, which is then hydrolyzed to a 3'-phosphate (3'-P) (By similarity).

If not degraded, poly(U) RNA would hybridize with poly(A) RNA tails and activate host dsRNA sensors (By similarity).

By similarity

2'-O-methyltransferase:

Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs. N7-methyl guanosine cap is a prerequisite for binding of nsp16. Therefore plays an essential role in viral mRNAs cap methylation which is essential to evade immune system.

By similarity

Miscellaneous

Isolate N2 belongs to genotype B.

Catalytic activityⁱ

Papain-like proteinase:
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal). EC:3.4.19.12

Cofactorⁱ

Uridylate-specific endoribonuclease:

Mn²⁺By similarityNote: Likely affects Nsp15 binding to RNA.By similarity

Sites

Feature key	Position(s)	DescriptionActions	Length
Active siteⁱ	1131	For PL1-PRO activityPROSITE-ProRule annotation	1
Active siteⁱ	1282	For PL1-PRO activityPROSITE-ProRule annotation	1
Active siteⁱ	1727	For PL2-PRO activityPROSITE-ProRule annotation	1
Active siteⁱ	1884	For PL2-PRO activityPROSITE-ProRule annotation	1
Active siteⁱ	3345	For 3CL-PRO activityPROSITE-ProRule annotation	1
Active siteⁱ	3449	For 3CL-PRO activityPROSITE-ProRule annotation	1
Metal bindingⁱ	4364	Zinc 1PROSITE-ProRule annotation	1
Metal bindingⁱ	4367	Zinc 1PROSITE-ProRule annotation	1
Metal bindingⁱ	4373	Zinc 1PROSITE-ProRule annotation	1
Metal bindingⁱ	4380	Zinc 1PROSITE-ProRule annotation	1
Metal bindingⁱ	4406	Zinc 2PROSITE-ProRule annotation	1
Metal bindingⁱ	4409	Zinc 2PROSITE-ProRule annotation	1
Metal bindingⁱ	4417	Zinc 2PROSITE-ProRule annotation	1
Metal bindingⁱ	4419	Zinc 2PROSITE-ProRule annotation	1
Active siteⁱ	5182	PROSITE-ProRule annotation	1
Active siteⁱ	5183	PROSITE-ProRule annotation	1
Active siteⁱ	5184	PROSITE-ProRule annotation	1
Metal bindingⁱ	5360	Zinc 3PROSITE-ProRule annotation	1
Metal bindingⁱ	5363	Zinc 3PROSITE-ProRule annotation	1
Metal bindingⁱ	5371	Zinc 4PROSITE-ProRule annotation	1
Metal bindingⁱ	5374	Zinc 3PROSITE-ProRule annotation	1
Metal bindingⁱ	5381	Zinc 3PROSITE-ProRule annotation	1
Metal bindingⁱ	5384	Zinc 4PROSITE-ProRule annotation	1
Metal bindingⁱ	5388	Zinc 4PROSITE-ProRule annotation	1
Metal bindingⁱ	5394	Zinc 4PROSITE-ProRule annotation	1
Metal bindingⁱ	5405	Zinc 5PROSITE-ProRule annotation	1
Metal bindingⁱ	5410	Zinc 5PROSITE-ProRule annotation	1
Metal bindingⁱ	5427	Zinc 5PROSITE-ProRule annotation	1
Metal bindingⁱ	5430	Zinc 5PROSITE-ProRule annotation	1
Active siteⁱ	6047	PROSITE-ProRule annotation	1
Active siteⁱ	6049	PROSITE-ProRule annotation	1
Active siteⁱ	6148	PROSITE-ProRule annotation	1
Metal bindingⁱ	6164	Zinc 6PROSITE-ProRule annotation	1
Metal bindingⁱ	6167	Zinc 6PROSITE-ProRule annotation	1
Metal bindingⁱ	6183	Zinc 6PROSITE-ProRule annotation	1
Metal bindingⁱ	6186	Zinc 6PROSITE-ProRule annotation	1
Metal bindingⁱ	6214	Zinc 7PROSITE-ProRule annotation	1
Metal bindingⁱ	6218	Zinc 7PROSITE-ProRule annotation	1
Metal bindingⁱ	6221	Zinc 7PROSITE-ProRule annotation	1
Active siteⁱ	6225	PROSITE-ProRule annotation	1
Active siteⁱ	6230	PROSITE-ProRule annotation	1
Metal bindingⁱ	6236	Zinc 7PROSITE-ProRule annotation	1
Metal bindingⁱ	6404	Zinc 8PROSITE-ProRule annotation	1
Metal bindingⁱ	6425	Zinc 8PROSITE-ProRule annotation	1
Metal bindingⁱ	6436	Zinc 8PROSITE-ProRule annotation	1
Metal bindingⁱ	6439	Zinc 8PROSITE-ProRule annotation	1
Active siteⁱ	6741	PROSITE-ProRule annotation	1
Active siteⁱ	6756	PROSITE-ProRule annotation	1
Active siteⁱ	6796	PROSITE-ProRule annotation	1
Active siteⁱ	6899	PROSITE-ProRule annotation	1
Active siteⁱ	6983	PROSITE-ProRule annotation	1
Active siteⁱ	7023	PROSITE-ProRule annotation	1
Active siteⁱ	7056	PROSITE-ProRule annotation	1

Regions

Feature key	Position(s)	DescriptionActions	Length
Zinc fingerⁱ	1208 – 1236	C4-type 1PROSITE-ProRule annotationAdd BLAST	29
Zinc fingerⁱ	1805 – 1841	C4-type 2PROSITE-ProRule annotationAdd BLAST	37
Zinc fingerⁱ	4364 – 4380	By similarityAdd BLAST	17
Zinc fingerⁱ	4406 – 4419	By similarityAdd BLAST	14
Nucleotide bindingⁱ	5636 – 5643	ATPBy similarity	8

GO - Molecular functionⁱ

ATP binding Source: UniProtKB-KW
ATP hydrolysis activity Source: RHEA
cysteine-type endopeptidase activity Source: InterPro
DNA helicase activity Source: UniProtKB-EC
endonuclease activity Source: UniProtKB-KW
exoribonuclease activity Source: InterPro
lyase activity Source: UniProtKB-KW
methyltransferase activity Source: UniProtKB-KW
RNA-directed 5'-3' RNA polymerase activity Source: UniProtKB-KW
RNA helicase activity Source: UniProtKB-EC
single-stranded RNA binding Source: InterPro
thiol-dependent deubiquitinase Source: UniProtKB-EC
zinc ion binding Source: InterPro

Complete GO annotation on QuickGO ...

GO - Biological processⁱ

induction by virus of catabolism of host mRNA Source: UniProtKB-KW
induction by virus of host autophagy Source: UniProtKB-KW
methylation Source: UniProtKB-KW
modulation by virus of host protein ubiquitination Source: UniProtKB-KW
suppression by virus of host gene expression Source: UniProtKB-KW
suppression by virus of host ISG15-protein conjugation Source: UniProtKB-KW
suppression by virus of host NF-kappaB cascade Source: UniProtKB-KW
suppression by virus of host type I interferon-mediated signaling pathway Source: UniProtKB-KW
transcription, DNA-templated Source: InterPro
viral genome replication Source: InterPro
viral protein processing Source: InterPro

Complete GO annotation on QuickGO ...

Keywordsⁱ

Molecular function	Endonuclease, Exonuclease, Helicase, Hydrolase, Lyase, Methyltransferase, Nuclease, Nucleotidyltransferase, Protease, RNA-binding, RNA-directed RNA polymerase, Thiol protease, Transferase
Biological process	Activation of host autophagy by virus, Decay of host mRNAs by virus, Eukaryotic host gene expression shutoff by virus, Eukaryotic host translation shutoff by virus, Host gene expression shutoff by virus, Host mRNA suppression by virus, Host-virus interaction, Inhibition of host innate immune response by virus, Inhibition of host interferon signaling pathway by virus, Inhibition of host ISG15 by virus, Inhibition of host NF-kappa-B by virus, Modulation of host ubiquitin pathway by viral deubiquitinase, Modulation of host ubiquitin pathway by virus, Ubl conjugation pathway, Viral immunoevasion, Viral RNA replication
Ligand	ATP-binding, Metal-binding, Nucleotide-binding, Zinc

Names & Taxonomyⁱ

Protein namesⁱ	Recommended name: Replicase polyprotein 1ab Short name: pp1ab Alternative name(s): ORF1ab polyprotein Cleaved into the following 15 chains: Host translation inhibitor nsp1 Short name: nsp1 Alternative name(s): p28 Non-structural protein 2 Short name: nsp2 Alternative name(s): p65 Papain-like proteinase (EC:3.4.19.12, EC:3.4.22.-) Short name: PL-PRO Alternative name(s): Non-structural protein 3 Short name: nsp3 p210 Non-structural protein 4 Short name: nsp4 Alternative name(s): Peptide HD2 p44 3C-like proteinase (EC:3.4.22.-) Short name: 3CL-PRO Short name: 3CLp Alternative name(s): M-PRO nsp5 p27 Non-structural protein 6 Short name: nsp6 Non-structural protein 7 Short name: nsp7 Alternative name(s): p10 Non-structural protein 8 Short name: nsp8 Alternative name(s): p22 Non-structural protein 9 Short name: nsp9 Alternative name(s): p12 Non-structural protein 10 Short name: nsp10 Alternative name(s): Growth factor-like peptide Short name: GFL p15 RNA-directed RNA polymerase (EC:2.7.7.48) Short name: Pol Short name: RdRp Alternative name(s): nsp12 p100 Helicase (EC:3.6.4.12, EC:3.6.4.13) Short name: Hel Alternative name(s): nsp13 p67 Guanine-N7 methyltransferase (EC:2.1.1.-, EC:3.1.13.-) Short name: ExoN Alternative name(s): nsp14 Uridylate-specific endoribonuclease (EC:4.6.1.-) Alternative name(s): NendoU nsp15 p35 2'-O-methyltransferase (EC:2.1.1.57) Alternative name(s): nsp16
Gene namesⁱ	Name:rep ORF Names:1a-1b
Organismⁱ	Human coronavirus HKU1 (isolate N2) (HCoV-HKU1)
Taxonomic identifierⁱ	443240 [NCBI]
Taxonomic lineageⁱ	Viruses › Riboviria › Orthornavirae › Pisuviricota › Pisoniviricetes › Nidovirales › Cornidovirineae › Coronaviridae › Orthocoronavirinae › Betacoronavirus › Embecovirus › Human coronavirus HKU1
Virus hostⁱ	Homo sapiens (Human) [TaxID: 9606]
Proteomesⁱ	UP000006551 Componentⁱ: Genome

Subcellular locationⁱ

Papain-like proteinase:

Non-structural protein 4:

Host membrane ; Multi-pass membrane protein
Host cytoplasm

Note:

Localizes in virally-induced cytoplasmic double-membrane vesicles.By similarity

Non-structural protein 6:

Host membrane Curated; Multi-pass membrane protein Curated

Non-structural protein 7:

host perinuclear region By similarity

Note:

nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes.

Non-structural protein 8:

host perinuclear region By similarity

Note:

nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes.

Non-structural protein 9:

host perinuclear region By similarity

Note:

nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes.

Non-structural protein 10:

host perinuclear region By similarity

Note:

nsp7, nsp8, nsp9 and nsp10 are localized in cytoplasmic foci, largely perinuclear. Late in infection, they merge into confluent complexes.

Helicase:

Host endoplasmic reticulum-Golgi intermediate compartment Curated

Note:

The helicase interacts with the N protein in membranous complexes and colocalizes with sites of synthesis of new viral RNA.

Uridylate-specific endoribonuclease:

host perinuclear region By similarity

Topology

Feature key	Position(s)	DescriptionActions	Length
Transmembraneⁱ	2196 – 2216	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	2257 – 2277	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	2288 – 2308	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	2371 – 2391	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	2413 – 2433	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	2814 – 2834	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	3089 – 3109	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	3121 – 3141	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	3148 – 3168	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	3173 – 3193	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	3621 – 3641	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	3646 – 3666	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	3671 – 3691	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	3714 – 3734	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	3742 – 3762	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	3770 – 3790	HelicalSequence analysisAdd BLAST	21
Transmembraneⁱ	3813 – 3833	HelicalSequence analysisAdd BLAST	21

Keywords - Cellular componentⁱ

Host cytoplasm, Host membrane, Membrane

PTM / Processingⁱ

Molecule processing

Feature key	Position(s)	DescriptionActions	Length
ChainⁱPRO_0000297773	1 – 222	Host translation inhibitor nsp1By similarityAdd BLAST	222
ChainⁱPRO_0000297774	223 – 809	Non-structural protein 2By similarityAdd BLAST	587
ChainⁱPRO_0000297775	810 – 2808	Papain-like proteinaseBy similarityAdd BLAST	1999
ChainⁱPRO_0000297776	2809 – 3304	Non-structural protein 4By similarityAdd BLAST	496
ChainⁱPRO_0000297777	3305 – 3607	3C-like proteinaseBy similarityAdd BLAST	303
ChainⁱPRO_0000297778	3608 – 3894	Non-structural protein 6By similarityAdd BLAST	287
ChainⁱPRO_0000297779	3895 – 3986	Non-structural protein 7By similarityAdd BLAST	92
ChainⁱPRO_0000297780	3987 – 4180	Non-structural protein 8By similarityAdd BLAST	194
ChainⁱPRO_0000297781	4181 – 4290	Non-structural protein 9By similarityAdd BLAST	110
ChainⁱPRO_0000297782	4291 – 4427	Non-structural protein 10By similarityAdd BLAST	137
ChainⁱPRO_0000297783	4428 – 5355	RNA-directed RNA polymeraseBy similarityAdd BLAST	928
ChainⁱPRO_0000297784	5356 – 5958	HelicaseBy similarityAdd BLAST	603
ChainⁱPRO_0000297785	5959 – 6479	Guanine-N7 methyltransferaseBy similarityAdd BLAST	521
ChainⁱPRO_0000297786	6480 – 6853	Uridylate-specific endoribonucleaseBy similarityAdd BLAST	374
ChainⁱPRO_0000297787	6854 – 7152	2'-O-methyltransferaseBy similarityAdd BLAST	299

Post-translational modificationⁱ

Specific enzymatic cleavages in vivo by its own proteases yield mature proteins. 3CL-PRO and PL-PRO proteinases are autocatalytically processed (By similarity).By similarity

Sites

Feature key	Position(s)	DescriptionActions	Length
Siteⁱ	222 – 223	Cleavage; by PL1-PROBy similarity	2
Siteⁱ	809 – 810	Cleavage; by PL1-PROBy similarity	2
Siteⁱ	2808 – 2809	Cleavage; by PL2-PROBy similarity	2
Siteⁱ	3304 – 3305	Cleavage; by 3CL-PROBy similarity	2
Siteⁱ	3607 – 3608	Cleavage; by 3CL-PROBy similarity	2
Siteⁱ	3894 – 3895	Cleavage; by 3CL-PROBy similarity	2
Siteⁱ	3986 – 3987	Cleavage; by 3CL-PROBy similarity	2
Siteⁱ	4180 – 4181	Cleavage; by 3CL-PROBy similarity	2
Siteⁱ	4290 – 4291	Cleavage; by 3CL-PROBy similarity	2
Siteⁱ	4427 – 4428	Cleavage; by 3CL-PROBy similarity	2
Siteⁱ	5355 – 5356	Cleavage; by 3CL-PROBy similarity	2
Siteⁱ	6479 – 6480	Cleavage; by 3CL-PROBy similarity	2
Siteⁱ	6853 – 6854	Cleavage; by 3CL-PROBy similarity	2

Interactionⁱ

Subunit structureⁱ

Nsp2 interacts with host PHB and PHB2. 3CL-PRO exists as monomer and homodimer. Nsp4 interacts with PL-PRO and nsp6. Only the homodimer shows catalytic activity. Eight copies of nsp7 and eight copies of nsp8 assemble to form a heterohexadecamer dsRNA-encircling ring structure. Nsp9 is a dimer. Nsp10 forms a dodecamer and interacts with nsp14 and nsp16; these interactions enhance nsp14 and nsp16 enzymatic activities. Nsp14 interacts (via N-terminus) with DDX1.

By similarity

Structureⁱ

3D structure databases

SMRⁱ	P0C6X3
ModBaseⁱ	Search...

Family & Domainsⁱ

Domains and Repeats

Feature key	Position(s)	DescriptionActions	Length
Domainⁱ	54 – 179	CoV Nsp1 globularPROSITE-ProRule annotationAdd BLAST	126
Domainⁱ	192 – 222	BetaCoV Nsp1 C-terminalPROSITE-ProRule annotationAdd BLAST	31
Domainⁱ	810 – 923	Ubiquitin-like 1PROSITE-ProRule annotationAdd BLAST	114
Repeatⁱ	945 – 954	1	10
Repeatⁱ	955 – 964	2	10
Repeatⁱ	965 – 974	3	10
Repeatⁱ	975 – 984	4	10
Repeatⁱ	985 – 994	5	10
Repeatⁱ	995 – 1004	6	10
Repeatⁱ	1005 – 1014	7	10
Repeatⁱ	1015 – 1024	8	10
Repeatⁱ	1025 – 1034	9	10
Repeatⁱ	1035 – 1044	10	10
Repeatⁱ	1045 – 1054	11	10
Domainⁱ	1093 – 1343	Peptidase C16 1PROSITE-ProRule annotationAdd BLAST	251
Domainⁱ	1321 – 1492	MacroPROSITE-ProRule annotationAdd BLAST	172
Domainⁱ	1548 – 1619	DPUPPROSITE-ProRule annotationAdd BLAST	72
Domainⁱ	1619 – 1674	Ubiquitin-like 2PROSITE-ProRule annotationAdd BLAST	56
Domainⁱ	1688 – 1948	Peptidase C16 2PROSITE-ProRule annotationAdd BLAST	261
Domainⁱ	1962 – 2063	Nucleic acid-bindingPROSITE-ProRule annotationAdd BLAST	102
Domainⁱ	3207 – 3304	Nsp4CPROSITE-ProRule annotationAdd BLAST	98
Domainⁱ	3305 – 3607	Peptidase C30PROSITE-ProRule annotationAdd BLAST	303
Domainⁱ	3895 – 3983	RdRp Nsp7 cofactorPROSITE-ProRule annotationAdd BLAST	89
Domainⁱ	3984 – 4180	RdRp Nsp8 cofactorPROSITE-ProRule annotationAdd BLAST	197
Domainⁱ	4181 – 4290	Nsp9 ssRNA-bindingPROSITE-ProRule annotationAdd BLAST	110
Domainⁱ	4291 – 4428	ExoN/MTase coactivatorPROSITE-ProRule annotationAdd BLAST	138
Domainⁱ	4433 – 4688	NiRANPROSITE-ProRule annotationAdd BLAST	256
Domainⁱ	4788 – 5355	Nsp12 RNA-dependent RNA polymerasePROSITE-ProRule annotationAdd BLAST	568
Domainⁱ	5035 – 5197	RdRp catalyticAdd BLAST	163
Domainⁱ	5356 – 5439	CV ZBDPROSITE-ProRule annotationAdd BLAST	84
Domainⁱ	5611 – 5792	(+)RNA virus helicase ATP-bindingAdd BLAST	182
Domainⁱ	5793 – 5962	(+)RNA virus helicase C-terminalAdd BLAST	170
Domainⁱ	6029 – 6244	ExoNPROSITE-ProRule annotationAdd BLAST	216
Domainⁱ	6253 – 6479	N7-MTasePROSITE-ProRule annotationAdd BLAST	227
Domainⁱ	6480 – 6540	Nsp15 N-terminal oligomerizationPROSITE-ProRule annotationAdd BLAST	61
Domainⁱ	6541 – 6661	AV-Nsp11N/CoV-Nsp15MPROSITE-ProRule annotationAdd BLAST	121
Domainⁱ	6711 – 6850	NendoUPROSITE-ProRule annotationAdd BLAST	140
Domainⁱ	6855 – 7149	Nidovirus-type SAM-dependent 2'-O-MTasePROSITE-ProRule annotationAdd BLAST	295

Region

Feature key	Position(s)	DescriptionActions	Length
Regionⁱ	945 – 1054	11 X 10 AA tandem repeat of N-[DN]-D-E-D-V-V-T-G-DAdd BLAST	110
Regionⁱ	947 – 1036	DisorderedSequence analysisAdd BLAST	90
Regionⁱ	2196 – 2433	HD1By similarityAdd BLAST	238
Regionⁱ	2814 – 3193	HD2By similarityAdd BLAST	380
Regionⁱ	3621 – 3833	HD3By similarityAdd BLAST	213
Regionⁱ	6288 – 6294	SAM-bindingPROSITE-ProRule annotation	7
Regionⁱ	6366 – 6380	GpppA-bindingPROSITE-ProRule annotationAdd BLAST	15

Domainⁱ

The hydrophobic domains (HD) could mediate the membrane association of the replication complex and thereby alter the architecture of the host cell membrane.

Sequence similaritiesⁱ

Belongs to the coronaviruses polyprotein 1ab family.Curated

Zinc finger

Feature key	Position(s)	DescriptionActions	Length
Zinc fingerⁱ	1208 – 1236	C4-type 1PROSITE-ProRule annotationAdd BLAST	29
Zinc fingerⁱ	1805 – 1841	C4-type 2PROSITE-ProRule annotationAdd BLAST	37
Zinc fingerⁱ	4364 – 4380	By similarityAdd BLAST	17
Zinc fingerⁱ	4406 – 4419	By similarityAdd BLAST	14

Keywords - Domainⁱ

Repeat, Transmembrane, Transmembrane helix, Zinc-finger

Family and domain databases

Conserved Domains Database More...CDDⁱ	cd21409, 1B_cv_Nsp13-like, 1 hit cd21560, betaCoV-Nsp6, 1 hit cd21659, betaCoV_Nsp14, 1 hit cd21666, betaCoV_Nsp5_Mpro, 1 hit cd20762, capping_2-OMTase_Nidovirales, 1 hit cd21519, cv_beta_Nsp2_MHV-like, 1 hit cd21473, cv_Nsp4_TM, 1 hit cd21593, HCoV_HKU1-like_RdRp, 1 hit cd21167, M_alpha_beta_cv_Nsp15-like, 1 hit cd21557, Macro_X_Nsp3-like, 1 hit cd21161, NendoU_cv_Nsp15-like, 1 hit cd21467, Ubl1_cv_Nsp3_N-like, 1 hit cd21466, Ubl2_cv_PLpro_N_Nsp3-like, 1 hit cd21401, ZBD_cv_Nsp13-like, 1 hit
Gene3Dⁱ	1.10.150.420, 1 hit 1.10.1840.10, 1 hit 1.10.8.1190, 2 hits 1.10.8.370, 1 hit 2.40.10.10, 2 hits 2.40.10.250, 1 hit 2.60.120.1680, 1 hit 3.10.20.350, 1 hit 3.10.20.540, 1 hit 3.30.160.820, 1 hit 3.30.70.3540, 1 hit 3.40.220.10, 1 hit 3.40.50.11020, 1 hit 3.40.50.11580, 1 hit 3.40.50.300, 2 hits
InterProⁱ	View protein in InterPro IPR027351, (+)RNA_virus_helicase_core_dom IPR022570, B-CoV_A_NSP1 IPR043608, CoV_NSP15_M IPR043606, CoV_NSP15_N IPR043613, CoV_NSP2_C IPR043611, CoV_NSP3_C IPR043612, CoV_NSP4_N IPR043502, DNA/RNA_pol_sf IPR041679, DNA2/NAM7-like_C IPR022733, DPUP_SUD_C_bCoV IPR037227, EndoU-like IPR002589, Macro_dom IPR043472, Macro_dom-like IPR044371, Macro_X_NSP3-like IPR042570, NAR_sf IPR043609, NendoU_nidovirus IPR044863, NIRAN IPR036333, NSP10_sf_CoV IPR044343, NSP13_1B_dom_CoV IPR027352, NSP13_ZBD_CoV-like IPR044315, NSP14_betaCoV IPR009466, NSP14_CoV IPR044322, NSP15_M_alpha_beta_CoV IPR043174, NSP15_middle_sf IPR042515, NSP15_N_CoV IPR044401, NSP15_NendoU_CoV IPR009461, NSP16_CoV-like IPR044384, NSP2_MHV-like IPR032592, NSP3_NAB_bCoV IPR044357, NSP3_Ubl1_dom_CoV IPR044353, Nsp3_Ubl2_dom_CoV IPR038083, NSP3A-like IPR032505, NSP4_C_CoV IPR038123, NSP4_C_sf_CoV IPR044367, NSP6_betaCoV IPR043610, NSP6_CoV IPR014828, NSP7_CoV IPR037204, NSP7_sf_CoV IPR014829, NSP8_CoV-like IPR037230, NSP8_sf_CoV IPR014822, NSP9_CoV IPR036499, NSP9_sf_CoV IPR027417, P-loop_NTPase IPR002705, Pept_C30/C16_B_coronavir IPR013016, Peptidase_C16_CoV IPR008740, Peptidase_C30_CoV IPR043477, Peptidase_C30_dom3_CoV IPR009003, Peptidase_S1_PA IPR043504, Peptidase_S1_PA_chymotrypsin IPR043177, PLpro_N_sf_CoV IPR043503, PLpro_palm_finger_dom_CoV IPR043178, PLpro_thumb_sf_CoV IPR044347, RdRp_HCoV_HKU1-like IPR001205, RNA-dir_pol_C IPR009469, RNA_pol_N_coronovir IPR018995, RNA_synth_NSP10_CoV IPR029063, SAM-dependent_MTases
Pfam protein domain database More...Pfamⁱ	View protein in Pfam PF13087, AAA_12, 1 hit PF16251, bCoV_NAR, 1 hit PF06471, CoV_ExoN, 1 hit PF06460, CoV_Methyltr_2, 1 hit PF09401, CoV_NSP10, 1 hit PF19215, CoV_NSP15_C, 1 hit PF19216, CoV_NSP15_M, 1 hit PF19219, CoV_NSP15_N, 1 hit PF19212, CoV_NSP2_C, 1 hit PF19218, CoV_NSP3_C, 1 hit PF16348, CoV_NSP4_C, 1 hit PF19217, CoV_NSP4_N, 1 hit PF19213, CoV_NSP6, 1 hit PF08716, CoV_NSP7, 1 hit PF08717, CoV_NSP8, 1 hit PF08710, CoV_NSP9, 1 hit PF08715, CoV_peptidase, 1 hit PF06478, CoV_RPol_N, 1 hit PF11963, DUF3477, 1 hit PF01661, Macro, 1 hit PF01831, Peptidase_C16, 1 hit PF05409, Peptidase_C30, 1 hit PF00680, RdRP_1, 1 hit
SMARTⁱ	View protein in SMART SM00506, A1pp, 1 hit
SUPFAMⁱ	SSF101816, SSF101816, 1 hit SSF140367, SSF140367, 1 hit SSF142877, SSF142877, 1 hit SSF143076, SSF143076, 1 hit SSF144246, SSF144246, 1 hit SSF159936, SSF159936, 1 hit SSF50494, SSF50494, 1 hit SSF52540, SSF52540, 1 hit SSF52949, SSF52949, 1 hit SSF53335, SSF53335, 1 hit SSF56672, SSF56672, 1 hit
PROSITEⁱ	View protein in PROSITE PS51961, AV_NSP11N_COV_NSP15M, 1 hit PS51963, BCOV_NSP1_C, 1 hit PS51942, BCOV_NSP3C_C, 1 hit PS51945, BCOV_NSP3E_NAB, 1 hit PS51952, COV_EXON_MTASE_COACT, 1 hit PS51954, COV_N7_MTASE, 1 hit PS51962, COV_NSP1, 1 hit PS51948, COV_NSP12_RDRP, 1 hit PS51960, COV_NSP15_NTD, 1 hit PS51943, COV_NSP3A_UBL, 1 hit PS51944, COV_NSP3D_UBL, 1 hit PS51946, COV_NSP4C, 1 hit PS51949, COV_NSP7, 1 hit PS51950, COV_NSP8, 1 hit PS51951, COV_NSP9_SSRNA_BD, 1 hit PS51653, CV_ZBD, 1 hit PS51442, M_PRO, 1 hit PS51154, MACRO, 1 hit PS51958, NENDOU, 1 hit PS51947, NIRAN, 1 hit PS51955, NIV_2_O_MTASE, 1 hit PS51953, NIV_EXON, 1 hit PS51124, PEPTIDASE_C16, 2 hits PS51657, PSRV_HELICASE, 1 hit

Sequences (2)ⁱ

Sequence statusⁱ: Complete.

Sequence processingⁱ: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsⁱ produced by ribosomal frameshifting. Align Add to basket

Isoform Replicase polyprotein 1ab (identifier: P0C6X3-1) [UniParc]FASTA Add to basket

Also known as: pp1ab

This isoform has been chosen as the canonicalⁱ sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

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        10         20         30         40         50
MIKTSKYGLG FKWAPEFRWL LPDAAEELAS PMKSDEGGLC PSTGQAMESV 
        60         70         80         90        100
GFVYDNHVKI DCRCILGQEW HVQSNLIRDI FVHEDLHVVE VLTKTAVKSG 
       110        120        130        140        150
TAILIKSPLH SLGGFPKGYV MGLFRSYKTK RYVVHHLSMT TSTTNFGEDF 
       160        170        180        190        200
LGWIVPFGFM PSYVHKWFQF CRLYIEESDL IISNFKFDDY DFSVEDAYAE 
       210        220        230        240        250
VHAEPKGKYS QKAYALLRQY RGIKPVLFVD QYGCDYSGKL ADCLQAYGHY 
       260        270        280        290        300
SLQDMRQKQS VWLANCDFDI VVAWHVVRDS RFVMRLQTIA TICGIKYVAQ 
       310        320        330        340        350
PTEDVVDGAV VIREPVHLLS ADAIVLKLPS LMKVMTHMDD FSIKSIYNVD 
       360        370        380        390        400
LCDCGFVMQY GYVDCFNDNC DFYGWVSGNM MDGFSCPLCC TVYDSSEVKA 
       410        420        430        440        450
QSSGVIPENP VLFTNSTDTV NPDSFNLYGY SVTPFGSCIY WSPRPGLWIP 
       460        470        480        490        500
IIKSSVKSYD DLVYSGVVGC KSIVKETALI THALYLDYVQ CKCGNLEQNH 
       510        520        530        540        550
ILGVNNSWCR QLLLNRGDYN MLLKNIDLFV KRRADFACKF AVCGDGFVPF 
       560        570        580        590        600
LLDGLIPRSY YLIQSGIFFT SLMSQFSQEV SDMCLKMCIL FMDRVSVATF 
       610        620        630        640        650
YIEHYVNRLV TQFKLLGTTL VNKMVNWFNT MLDASAPATG WLLYQLLNGL 
       660        670        680        690        700
FVVSQANFNF VALIPDYAKI LVNKFYTFFK LLLECVTVDV LKDMPVLKTI 
       710        720        730        740        750
NGLVCIVGNK FYNVSTGLIP GFVLPCNAQE QQIYFFEGVA ESVIVEDDVI 
       760        770        780        790        800
ENVKSSLSSY EYCQPPKSVE KICIIDNMYM GKCGDKFFPI VMNDKNICLL 
       810        820        830        840        850
DQAWRFPCAG RKVNFNEKPV VMEIPSLMTV KVMFDLDSTF DDILGKVCSE 
       860        870        880        890        900
FEVEKGVTVD DFVAVVCDAI ENALNSCKDH PVVGYQVRAF LNKLNENVVY 
       910        920        930        940        950
LFDEAGDEAM ASRMYCTFAI EDVEDVISSE AVEDTIDGVV EDTINDDEDV 
       960        970        980        990       1000
VTGDNDDEDV VTGDNDDEDV VTGDNDDEDV VTGDNDDEDV VTGDNDDEDV 
      1010       1020       1030       1040       1050
VTGDNDDEDV VTGDNDDEDV VTGDNDDEDV VTGDNDDEDV VTGDNDDEDV 
      1060       1070       1080       1090       1100
VTGDNDDEEI VTGDNDDQIV VTGDDVDDIE SVYDFDTYKA LLVFNDVYND 
      1110       1120       1130       1140       1150
ALFVSYGSSV ETETYFKVNG LWSPTITHTN CWLRSVLLVM QKLPFKFKDL 
      1160       1170       1180       1190       1200
AIENMWLSYK VGYNQSFVDY LLTTIPKAIV LPQGGYVADF AYWFLNQFDI 
      1210       1220       1230       1240       1250
NAYANWCCLK CGFSFDLNGL DAVFFYGDIV SHVCKCGHNM TLIAADLPCT 
      1260       1270       1280       1290       1300
LHFSLFDDNF CAFCTPKKIF IAACAVDVNV CHSVAVIGDE QIDGKFVTKF 
      1310       1320       1330       1340       1350
SGDKFDFIVG YGMSFSMSSF ELAQLYGLCI TPNVCFVKGD IINVARLVKA 
      1360       1370       1380       1390       1400
DVIVNPANGH MLHGGGVAKA IAVAAGKKFS KETAAMVKSK GVCQVGDCYV 
      1410       1420       1430       1440       1450
STGGKLCKTI LNIVGPDARQ DGRQSYVLLA RAYKHLNNYD CCLSTLISAG 
      1460       1470       1480       1490       1500
IFSVPADVSL TYLLGVVDKQ VILVSNNKED FDIIQKCQIT SVVGTKALAV 
      1510       1520       1530       1540       1550
RLTANVGRVI KFETDAYKLF LSGDDCFVSN SSVIQEVLLL RHDIQLNNDV 
      1560       1570       1580       1590       1600
RDYLLSKMTS LPKDWRLINK FDVINGVKTV KYFECPNSIY ICSQGKDFGY 
      1610       1620       1630       1640       1650
VCDGSFYKAT VNQVCVLLAK KIDVLLTVDG VNFKSISLTV GEVFGKILGN 
      1660       1670       1680       1690       1700
VFCDGIDVTK LKCSDFYADK ILYQYENLSL ADISAVQSSF GFDQQQLLAY 
      1710       1720       1730       1740       1750
YNFLTVCKWS VVVNGPFFSF EQSHNNCYVN VACLMLQHIN LKFNKWQWQE 
      1760       1770       1780       1790       1800
AWYEFRAGRP HRLVALVLAK GHFKFDEPSD ATDFIRVVLK QADLSGAICE 
      1810       1820       1830       1840       1850
LELICDCGIK QESRVGVDAV MHFGTLAKTD LFNGYKIGCN CAGRIVHCTK 
      1860       1870       1880       1890       1900
LNVPFLICSN TPLSKDLPDD VVAANMFMGV GVGHYTHLKC GSPYQHYDAC 
      1910       1920       1930       1940       1950
SVKKYTGVSG CLTDCLYLKN LTQTFTSMLT NYFLDDVEMV AYNPDLSQYY 
      1960       1970       1980       1990       2000
CDNGKYYTKP IIKAQFKPFA KVDGVYTNFK LVGHDICAQL NDKLGFNVDL 
      2010       2020       2030       2040       2050
PFVEYKVTVW PVATGDVVLA SDDLYVKRYF KGCETFGKPV IWLCHDEASL 
      2060       2070       2080       2090       2100
NSLTYFNKPS FKSENRYSVL SVDSVSEESQ GNVVTSVMES QISTKEVKLK 
      2110       2120       2130       2140       2150
GVRKTVKIED AIIVNDENSS IKVVKSLSLV DVWDMYLTGC DYVVWVANEL 
      2160       2170       2180       2190       2200
SRLVKSPTVR EYIRYGIKPI TIPIDLLCLR DDNQTLLVPK IFKARAIEFY 
      2210       2220       2230       2240       2250
GFLKWLFIYV FSLLHFTNDK TIFYTTEIAS KFTFNLFCLA LKNAFQTFRW 
      2260       2270       2280       2290       2300
SIFIKGFLVV ATVFLFWFNF LYINVIFSDF YLPNISVFPI FVGRIVMWIK 
      2310       2320       2330       2340       2350
ATFGLVTICD FYSKLGVGFT SHFCNGSFIC ELCYSGFDML DTYAAIDFVQ 
      2360       2370       2380       2390       2400
YEVDRRVLFD YVSLVKLIVE LVIGYSLYTV WFYPLFCLIG LQLFTTWLPD 
      2410       2420       2430       2440       2450
LFMLETMHWL IRFIVFVANM LPAFVLLRFY IVVTAMYKVV GFIRHIVYGC 
      2460       2470       2480       2490       2500
NKAGCLFCYK RNCSVRVKCS TIVGGVIRYY DITANGGTGF CVKHQWNCFN 
      2510       2520       2530       2540       2550
CHSFKPGNTF ITVEAAIELS KELKRPVNPT DASHYVVTDI KQVGCMMRLF 
      2560       2570       2580       2590       2600
YDRDGQRVYD DVDASLFVDI NNLLHSKVKV VPNLYVVVVE SDADRANFLN 
      2610       2620       2630       2640       2650
AVVFYAQSLY RPILLVDKKL ITTACNGISV TQTMFDVYVD TFMSHFDVDR 
      2660       2670       2680       2690       2700
KSFNNFVNIA HASLREGVQL EKVLDTFVGC VRKCCSIDSD VETRFITKSM 
      2710       2720       2730       2740       2750
ISAVAAGLEF TDENYNNLVP TYLKSDNIVA ADLGVLIQNG AKHVQGNVAK 
      2760       2770       2780       2790       2800
AANISCIWFI DTFNQLTADL QHKLKKACVK TGLKLKLTFN KQEASVPILT 
      2810       2820       2830       2840       2850
TPFSLKGGVV LSNLLYILFF ISLICFILLW ALLPTYSVYK SDIHLPAYAS 
      2860       2870       2880       2890       2900
FKVIDNGVVR DISVNDLCFA NKFFQFDQWY ESTFGSFYYH NSMDCPIVVA 
      2910       2920       2930       2940       2950
VMDEDIGSTM FNVPTKVLRH GFHVLHFLTY AFASDSVQCY TPHIQISYND 
      2960       2970       2980       2990       3000
FYASGCVLSS LCTMFKRGDG TPHPYCYSDG VMKNASLYTS LVPHTRYSLA 
      3010       3020       3030       3040       3050
NSNGFIRFPD VISEGIVRIV RTRSMTYCRV GACEYAEEGI CFNFNSSWVL 
      3060       3070       3080       3090       3100
NNDYYRSMPG TFCGRDLFDL FYQFFSSLIR PIDFFSLTAS SIFGAILAIV 
      3110       3120       3130       3140       3150
VVLVFYYLIK LKRAFGDYTS VVVINVIVWC INFLMLFVFQ VYPICACVYA 
      3160       3170       3180       3190       3200
CFYFYVTLYF PSEISVIMHL QWIVMYGAIM PFWFCVTYVA MVIANHVLWL 
      3210       3220       3230       3240       3250
FSYCRKIGVN VCNDSTFEET SLTTFMITKD SYCRLKNSVS DVAYNRYLSL 
      3260       3270       3280       3290       3300
YNKYRYYSGK MDTAAYREAA CSQLAKAMET FNHNNGNDVL YQPPTASVST 
      3310       3320       3330       3340       3350
SFLQSGIVKM VSPTSKIEPC IVSVTYGSMT LNGLWLDDKV YCPRHVICLS 
      3360       3370       3380       3390       3400
SNMNEPDYSA LLCRVTLGDF TIMSGRMSLT VVSYQMQGCQ LVLTVSLQNP 
      3410       3420       3430       3440       3450
YTPKYTFGVV KPGETFTVLA AYNGRPQGAF HVTMRSSYTI KGSFLCGSCG 
      3460       3470       3480       3490       3500
SVGYVLTGDS VKFVYMHQLE LSTGCHTGTD FTGNFYGPYR DAQVVQLPVK 
      3510       3520       3530       3540       3550
DYVQTVNVIA WLYAAILNNC AWFVQNDVCS IEDFNVWAMT NGFSQVKADL 
      3560       3570       3580       3590       3600
VLDALASMTG VSIETLLAAI KRLYMGFQGR QILGSCTFED ELAPSDVYQQ 
      3610       3620       3630       3640       3650
LAGVKLQSKT KRFIKETIYW ILISTFLFSC IISAFVKWTI FMYINTHMIG 
      3660       3670       3680       3690       3700
VTLCVLCFVS FMMLLVKHKH FYLTMYIIPV LCTLFYVNYL VVYKEGFRGL 
      3710       3720       3730       3740       3750
TYVWLSYFVP AVNFTYVYEV FYGCILCVFA IFITMHSINH DIFSLMFLVG 
      3760       3770       3780       3790       3800
RIVTLISMWY FGSNLEEDVL LFITAFLGTY TWTTILSLAI AKIVANWLSV 
      3810       3820       3830       3840       3850
NIFYFTDVPY IKLILLSYLF IGYILSCYWG FFSLLNSVFR MPMGVYNYKI 
      3860       3870       3880       3890       3900
SVQELRYMNA NGLRPPRNSF EAILLNLKLL GIGGVPVIEV SQIQSKLTDV 
      3910       3920       3930       3940       3950
KCANVVLLNC LQHLHVASNS RLWQYCSILH NEILSTSDLS VAFDKLAQLL 
      3960       3970       3980       3990       4000
IVLFANPAAV DTKCLASIDE VSDDYVQDST VLQALQSEFV NMASFVEYEV 
      4010       4020       4030       4040       4050
AKKNLADAKN SGSVNQQQIK QLEKACNIAK SVYERDKAVA RKLERMADLA 
      4060       4070       4080       4090       4100
LTNMYKEARI NDKKSKVVSA LQTMLFSMVR KLDNQALNSI LDNAVKGCVP 
      4110       4120       4130       4140       4150
LNAIPALAAN TLTIIIPDKQ VFDKVVDNVY VAYAGSVWHI QTVQDADGIN 
      4160       4170       4180       4190       4200
KQLTDISVDS NWPLVIIANR YNEVANAVMQ NNELMPHKLK IQVVNSGSDM 
      4210       4220       4230       4240       4250
NCNIPTQCYY NNGSSGRIVY AVLSDVDGLK YTKIIKDDGN CVVLELDPPC 
      4260       4270       4280       4290       4300
KFSIQDVKGL KIKYLYFIKG CNTLARGWVV GTLSSTIRLQ AGVATEYAAN 
      4310       4320       4330       4340       4350
SSILSLCAFS VDPKKTYLDY IQQGGVPIIN CVKMLCDHAG TGMAITIKPE 
      4360       4370       4380       4390       4400
ATINQDSYGG ASVCIYCRAR VEHPDVDGLC KLRGKFVQVP LGIKDPILYV 
      4410       4420       4430       4440       4450
LTHDVCQVCG FWRDGSCSCV GSGVAVQSKD LNFLNRVRGT SVNARLVPCA 
      4460       4470       4480       4490       4500
SGLSTDVQLR AFDICNTNRA GIGLYYKVNC CRFQRIDDDG NKLDKFFVVK 
      4510       4520       4530       4540       4550
RTNLEVYNKE KTYYELTKSC GVVAEHDFFT FDIDGSRVPH IVRKNLSKYT 
      4560       4570       4580       4590       4600
MLDLCYALRH FDCNDCSVLC EILCEYADCK ESYFSKKDWY DFVENPDIIN 
      4610       4620       4630       4640       4650
IYKKLGPIFN RALLNTVSFA DTLVKVGLVG VLTLDNQDLY GQWYDFGDFI 
      4660       4670       4680       4690       4700
QTAPGFGVAV ADSYYSYMMP MLTMCHVLDC ELFVNDSYRQ FDLVQYDFTD 
      4710       4720       4730       4740       4750
YKLELFNKYF KYWGMKYHPN TVDCDNDRCI IHCANFNILF SMVLPNTCFG 
      4760       4770       4780       4790       4800
PLVRQIFVDG VPFVVSIGYH YKELGVVMNL DVDTHRYRLS LKDLLLYAAD 
      4810       4820       4830       4840       4850
PAMHVASASA LLDLRTCCFS VAAITSGIKF QTVKPGNFNQ DFYEFVKSKG 
      4860       4870       4880       4890       4900
LFKEGSTVDL KHFFFTQDGN AAITDYNYYK YNLPTMVDIK QLLFVLEVVY 
      4910       4920       4930       4940       4950
KYFEIYDGGC IPASQVIVNN YDKSAGYPFN KFGKARLYYE ALSFEEQNEI 
      4960       4970       4980       4990       5000
YAYTKRNVLP TLTQMNLKYA ISAKNRARTV AGVSILSTMT GRMFHQKCLK 
      5010       5020       5030       5040       5050
SIAATRGVPV VIGTTKFYGG WDDMLRHLIK DVDNPVLMGW DYPKCDRAMP 
      5060       5070       5080       5090       5100
NILRIVSSLV LARKHEFCCS HGDRFYRLAN ECAQVLSEIV MCGGCYYVKP 
      5110       5120       5130       5140       5150
GGTSSGDATT AFANSVFNIC QAVTANVCSL MACNGHKIED LSIRNLQKRL 
      5160       5170       5180       5190       5200
YSNVYRTDYV DYTFVNEYYE FLCKHFSMMI LSDDGVVCYN SDYASKGYIA 
      5210       5220       5230       5240       5250
NISVFQQVLY YQNNVFMSES KCWVENDITN GPHEFCSQHT MLVKIDGDYV 
      5260       5270       5280       5290       5300
YLPYPDPSRI LGAGCFVDDL LKTDSVLLIE RFVSLAIDAY PLVHHENEEY 
      5310       5320       5330       5340       5350
QKVFRVYLEY IKKLYNDLGN QILDSYSVIL STCDGLKFTD ESFYKNMYLK 
      5360       5370       5380       5390       5400
SAVMQSVGAC VVCSSQTSLR CGSCIRKPLL CCKCCYDHVM ATNHKYVLSV 
      5410       5420       5430       5440       5450
SPYVCNAPNC DVSDVTKLYL GGMSYYCENH KPHYSFKLVM NGMVFGLYKQ 
      5460       5470       5480       5490       5500
SCTGSPYIDD FNKIASCKWT EVDDYVLANE CIERLKLFAA ETQKATEEAF 
      5510       5520       5530       5540       5550
KQSYASATIQ EIVSDREIIL CWETGKVKPP LNKNYVFTGY HFTSTGKTVL 
      5560       5570       5580       5590       5600
GEYVFDKSEL TNGVYYRATT TYKLSIGDVF VLTSHSVANL SAPTLVPQEN 
      5610       5620       5630       5640       5650
YASIRFSSVY SVPLLFQTNV ANYQHIGMKR YCTVQGPPGT GKSHLAIGLA 
      5660       5670       5680       5690       5700
VYYYTARVVY TAASHAAVDA LCEKAYKFLN INDCTRIIPA KVRVDCYDKF 
      5710       5720       5730       5740       5750
KINDTTCKYV FTTINALPEL VTDIVVVDEV SMLTNYELSV INARVKAKHY 
      5760       5770       5780       5790       5800
VYIGDPAQLP APRVLLSKGS LEPRHFNSIT KIMCCLGPDI FLGNCYRCPK 
      5810       5820       5830       5840       5850
EIVETVSALV YDNKLKAKND NSSLCFKVYF KGQTTHESSS AVNIQQIYLI 
      5860       5870       5880       5890       5900
SKFLKANPVW NSAVFISPYN SQNYVAKRIL GVQTQTVDSA QGSEYDYVIY 
      5910       5920       5930       5940       5950
SQTAETAHSI NVNRFNVAIT RAKKGIFCVM SNMQLFESLN FITLPLDKIQ 
      5960       5970       5980       5990       6000
NQTLSRLHCT TNLFKDCSKN FLGYHPAHAP SFLSVDDKYK VNEDLAVCLN 
      6010       6020       6030       6040       6050
ICEPVLTYSR LISLMGFKLD LTLDGYSKFF ITKDEAIKRV RGWVGFDVEG 
      6060       6070       6080       6090       6100
AHATRDNIGT NFPLQIGFST GVDFVVEATG LFAERDCYIF KRTVAKAPPG 
      6110       6120       6130       6140       6150
DNFKHLIPLM SKGQKWDVVR IRIVQMLSDY LLDLSDSVVF ITWSASFELT 
      6160       6170       6180       6190       6200
CLRYFAKLGR ELNCDVCPNR ATCYNSRTGY YGCWRHSYTC DYVYNPLIVD 
      6210       6220       6230       6240       6250
IQQWGYTGSL TSNHDIICNV HKGAHVASSD AIMTRCLAIY DCFCKSVNWN 
      6260       6270       6280       6290       6300
LEYPIISNEV SINTSCRLLQ RVMLKAAMLC NRYNLCYDIG NPKGIACVKD 
      6310       6320       6330       6340       6350
YEFKFYDASP VVKSVKQLFY VYDVHKDNFK DGLCMFWNCN VDKYPSNSIV 
      6360       6370       6380       6390       6400
CRFDTRVLNK LNLPGCNGGS LYVNKHAFHT NPFTRTVFEN LKPMPFFYYS 
      6410       6420       6430       6440       6450
DTPCVYVDGL ESKQVDYVPL RSATCITRCN LGGAVCSKHA EDYCKYLESY 
      6460       6470       6480       6490       6500
NVATTAGFTF WVYKTFDFYN LWNTFTMLQS LENVIYNLVN AGHYDGRIGE 
      6510       6520       6530       6540       6550
LPCAIMNDKV VVKINNVDTV IFKNNTSLPT NIAVELFTKR SIRHHPELKI 
      6560       6570       6580       6590       6600
LRNLNIDICW KHVLWDYVKD SLFCSSTYGV CKYTDLNFIE NLNVLFDGRD 
      6610       6620       6630       6640       6650
NGALEAFRKA RNGVFISTGK LSSLSMIKGP QRADLNGVIV DKVGELNVEF 
      6660       6670       6680       6690       6700
WFAMRKDGDD VIFSRADSLS PSHYWSPQGN LGGNCAGNAS GNDALARFTI 
      6710       6720       6730       6740       6750
FTQSRVLSTF EPRSDLERDF IDMEDSLFIA KYGLEDYAFD HIVYGSFNYK 
      6760       6770       6780       6790       6800
VIGGLHLLIG LFRRLKKSNL VIQEFLQYDS SIHSYFITDQ ECGSSKSVCT 
      6810       6820       6830       6840       6850
VIDLLLDDFV VIVKSLNLNC VSKVVNINVD FKDFQFMLWC NDNKIMTFYP 
      6860       6870       6880       6890       6900
KMQATSDWKP GYSMPVLYKY LNVPLERVSL WNYGKAINLP TGCMMNVAKY 
      6910       6920       6930       6940       6950
TQLCQYLNTT TLAVPVNMRV LHLGAGSDKE VAPGSAVLRQ WLPSGSILVD 
      6960       6970       6980       6990       7000
NDLNPFVSDS LVTYFGDCMT LPFDCHWDLI ISDMYDPLTK NIGDYNVSKD 
      7010       7020       7030       7040       7050
GFFTYICYLI RDKLSLGGSV AIKITEFSWN ADLYKLMSYF AFWTVFCTNV 
      7060       7070       7080       7090       7100
NASSSEGFLI GINYLGKSCF EIDGNVMHAN YLFWRNSTTW NGGAYSLFDM 
      7110       7120       7130       7140       7150
SKFSLKLAGT AVVNLRPDQL NDLVYSLIER GKLLVRDTRK EIFVGDSLVN 

TC

Note: Produced by -1 ribosomal frameshifting at the 1a-1b genes boundary.

Length:7,152

Mass (Da):807,495

Last modified:June 10, 2008 - v1

Checksum:ⁱ1B6E93484EF69631

GO

Isoform Replicase polyprotein 1a (identifier: P0C6U4-1) [UniParc]FASTA Add to basket

Also known as: pp1a, ORF1a polyprotein

The sequence of this isoform can be found in the external entry P0C6U4.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Length:4,441

Mass (Da):499,423

GO

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	AY884001 Genomic RNA Translation: AAX76519.1

Select the link destinations:
EMBLⁱ
GenBankⁱ
DDBJⁱ

Links Updated

AY884001 Genomic RNA Translation: AAX76519.1

Keywords - Coding sequence diversityⁱ

Ribosomal frameshifting

Protein	Similar proteins		Species	Score	Length	Source
P0C6X3	ORF1ab polyprotein		CVHK1		7152	UniRef100_P0C6X3

Protein	Similar proteins		Species	Score	Length	Source
P0C6X3	ORF1ab polyprotein		CVHK1		7152	UniRef90_P0C6X3
ORF1ab polyprotein		CVHK1		7152
ORF1ab polyprotein (Fragment)		CVHK1		928
ORF1ab polyprotein		CVHK1		7146
ORF1ab polyprotein		CVHK1		7142
+2

Protein	Similar proteins		Species	Score	Length	Source
P0C6X3	Replicase polyprotein 1ab	)	CVHOC		7095	UniRef50_P0C6X6
Replicase polyprotein 1ab		CVBM		7094
Replicase polyprotein 1ab		CVBEN		7094
Replicase polyprotein 1ab		CVBLU		7094
Replicase polyprotein 1ab		CVBQ		7059
+1230

Cross-referencesⁱ

Sequence databases

Select the link destinations: EMBLⁱ GenBankⁱ DDBJⁱ Links Updated	AY884001 Genomic RNA Translation: AAX76519.1

Select the link destinations:
EMBLⁱ
GenBankⁱ
DDBJⁱ

Links Updated

AY884001 Genomic RNA Translation: AAX76519.1

3D structure databases

SMRⁱ	P0C6X3
ModBaseⁱ	Search...

Family and domain databases

CDDⁱ	cd21409, 1B_cv_Nsp13-like, 1 hit cd21560, betaCoV-Nsp6, 1 hit cd21659, betaCoV_Nsp14, 1 hit cd21666, betaCoV_Nsp5_Mpro, 1 hit cd20762, capping_2-OMTase_Nidovirales, 1 hit cd21519, cv_beta_Nsp2_MHV-like, 1 hit cd21473, cv_Nsp4_TM, 1 hit cd21593, HCoV_HKU1-like_RdRp, 1 hit cd21167, M_alpha_beta_cv_Nsp15-like, 1 hit cd21557, Macro_X_Nsp3-like, 1 hit cd21161, NendoU_cv_Nsp15-like, 1 hit cd21467, Ubl1_cv_Nsp3_N-like, 1 hit cd21466, Ubl2_cv_PLpro_N_Nsp3-like, 1 hit cd21401, ZBD_cv_Nsp13-like, 1 hit
Gene3Dⁱ	1.10.150.420, 1 hit 1.10.1840.10, 1 hit 1.10.8.1190, 2 hits 1.10.8.370, 1 hit 2.40.10.10, 2 hits 2.40.10.250, 1 hit 2.60.120.1680, 1 hit 3.10.20.350, 1 hit 3.10.20.540, 1 hit 3.30.160.820, 1 hit 3.30.70.3540, 1 hit 3.40.220.10, 1 hit 3.40.50.11020, 1 hit 3.40.50.11580, 1 hit 3.40.50.300, 2 hits
InterProⁱ	View protein in InterPro IPR027351, (+)RNA_virus_helicase_core_dom IPR022570, B-CoV_A_NSP1 IPR043608, CoV_NSP15_M IPR043606, CoV_NSP15_N IPR043613, CoV_NSP2_C IPR043611, CoV_NSP3_C IPR043612, CoV_NSP4_N IPR043502, DNA/RNA_pol_sf IPR041679, DNA2/NAM7-like_C IPR022733, DPUP_SUD_C_bCoV IPR037227, EndoU-like IPR002589, Macro_dom IPR043472, Macro_dom-like IPR044371, Macro_X_NSP3-like IPR042570, NAR_sf IPR043609, NendoU_nidovirus IPR044863, NIRAN IPR036333, NSP10_sf_CoV IPR044343, NSP13_1B_dom_CoV IPR027352, NSP13_ZBD_CoV-like IPR044315, NSP14_betaCoV IPR009466, NSP14_CoV IPR044322, NSP15_M_alpha_beta_CoV IPR043174, NSP15_middle_sf IPR042515, NSP15_N_CoV IPR044401, NSP15_NendoU_CoV IPR009461, NSP16_CoV-like IPR044384, NSP2_MHV-like IPR032592, NSP3_NAB_bCoV IPR044357, NSP3_Ubl1_dom_CoV IPR044353, Nsp3_Ubl2_dom_CoV IPR038083, NSP3A-like IPR032505, NSP4_C_CoV IPR038123, NSP4_C_sf_CoV IPR044367, NSP6_betaCoV IPR043610, NSP6_CoV IPR014828, NSP7_CoV IPR037204, NSP7_sf_CoV IPR014829, NSP8_CoV-like IPR037230, NSP8_sf_CoV IPR014822, NSP9_CoV IPR036499, NSP9_sf_CoV IPR027417, P-loop_NTPase IPR002705, Pept_C30/C16_B_coronavir IPR013016, Peptidase_C16_CoV IPR008740, Peptidase_C30_CoV IPR043477, Peptidase_C30_dom3_CoV IPR009003, Peptidase_S1_PA IPR043504, Peptidase_S1_PA_chymotrypsin IPR043177, PLpro_N_sf_CoV IPR043503, PLpro_palm_finger_dom_CoV IPR043178, PLpro_thumb_sf_CoV IPR044347, RdRp_HCoV_HKU1-like IPR001205, RNA-dir_pol_C IPR009469, RNA_pol_N_coronovir IPR018995, RNA_synth_NSP10_CoV IPR029063, SAM-dependent_MTases
Pfamⁱ	View protein in Pfam PF13087, AAA_12, 1 hit PF16251, bCoV_NAR, 1 hit PF06471, CoV_ExoN, 1 hit PF06460, CoV_Methyltr_2, 1 hit PF09401, CoV_NSP10, 1 hit PF19215, CoV_NSP15_C, 1 hit PF19216, CoV_NSP15_M, 1 hit PF19219, CoV_NSP15_N, 1 hit PF19212, CoV_NSP2_C, 1 hit PF19218, CoV_NSP3_C, 1 hit PF16348, CoV_NSP4_C, 1 hit PF19217, CoV_NSP4_N, 1 hit PF19213, CoV_NSP6, 1 hit PF08716, CoV_NSP7, 1 hit PF08717, CoV_NSP8, 1 hit PF08710, CoV_NSP9, 1 hit PF08715, CoV_peptidase, 1 hit PF06478, CoV_RPol_N, 1 hit PF11963, DUF3477, 1 hit PF01661, Macro, 1 hit PF01831, Peptidase_C16, 1 hit PF05409, Peptidase_C30, 1 hit PF00680, RdRP_1, 1 hit
SMARTⁱ	View protein in SMART SM00506, A1pp, 1 hit
SUPFAMⁱ	SSF101816, SSF101816, 1 hit SSF140367, SSF140367, 1 hit SSF142877, SSF142877, 1 hit SSF143076, SSF143076, 1 hit SSF144246, SSF144246, 1 hit SSF159936, SSF159936, 1 hit SSF50494, SSF50494, 1 hit SSF52540, SSF52540, 1 hit SSF52949, SSF52949, 1 hit SSF53335, SSF53335, 1 hit SSF56672, SSF56672, 1 hit
PROSITEⁱ	View protein in PROSITE PS51961, AV_NSP11N_COV_NSP15M, 1 hit PS51963, BCOV_NSP1_C, 1 hit PS51942, BCOV_NSP3C_C, 1 hit PS51945, BCOV_NSP3E_NAB, 1 hit PS51952, COV_EXON_MTASE_COACT, 1 hit PS51954, COV_N7_MTASE, 1 hit PS51962, COV_NSP1, 1 hit PS51948, COV_NSP12_RDRP, 1 hit PS51960, COV_NSP15_NTD, 1 hit PS51943, COV_NSP3A_UBL, 1 hit PS51944, COV_NSP3D_UBL, 1 hit PS51946, COV_NSP4C, 1 hit PS51949, COV_NSP7, 1 hit PS51950, COV_NSP8, 1 hit PS51951, COV_NSP9_SSRNA_BD, 1 hit PS51653, CV_ZBD, 1 hit PS51442, M_PRO, 1 hit PS51154, MACRO, 1 hit PS51958, NENDOU, 1 hit PS51947, NIRAN, 1 hit PS51955, NIV_2_O_MTASE, 1 hit PS51953, NIV_EXON, 1 hit PS51124, PEPTIDASE_C16, 2 hits PS51657, PSRV_HELICASE, 1 hit
MobiDBⁱ	Search...

Entry informationⁱ

Entry nameⁱ	R1AB_CVHN2
Accessionⁱ	P0C6X3Primary (citable) accession number: P0C6X3 Secondary accession number(s): Q14EB2
Entry historyⁱ	Integrated into UniProtKB/Swiss-Prot:	June 10, 2008
	Last sequence update:	June 10, 2008
	Last modified:	February 23, 2022
	This is version 95 of the entry and version 1 of the sequence. See complete history.
Entry statusⁱ	Reviewed (UniProtKB/Swiss-Prot)
Annotation program	Viral Protein Annotation Program

Miscellaneousⁱ

Documents

SIMILARITY comments
Index of protein domains and families

UniProtKB

UniParc

Help

UniRef

Proteomes

Annotation systems

Supporting data

UniProtKB - P0C6X3 (R1AB_CVHN2)

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Replicase polyprotein 1ab

Select a section on the left to see content.

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Miscellaneous

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

Sites

Regions

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Topology

Keywords - Cellular componenti

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Sites

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Region

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Zinc finger

Keywords - Domaini

Family and domain databases

Sequence databases

Keywords - Coding sequence diversityi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

3D structure databases

Family and domain databases

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

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Functionⁱ

Catalytic activityⁱ

GO - Molecular functionⁱ

GO - Biological processⁱ

Names & Taxonomyⁱ

Subcellular locationⁱ

Keywords - Cellular componentⁱ

PTM / Processingⁱ

Interactionⁱ

Structureⁱ

Family & Domainsⁱ

Sequence similaritiesⁱ

Keywords - Domainⁱ

Keywords - Coding sequence diversityⁱ

Cross-referencesⁱ

Entry informationⁱ

Miscellaneousⁱ