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Protein

Major capsid protein VP1

Gene
N/A
Organism
JC polyomavirus (JCPyV) (JCV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Forms an icosahedral capsid with a T=7 symmetry and a 40 nm diameter. The capsid is composed of 72 pentamers linked to each other by disulfide bonds and associated with VP2 or VP3 proteins. Interacts with a N-linked glycoprotein containing terminal alpha(2-6)-linked sialic acids on the cell surface to provide virion attachment to target cell. The serotonergic receptor 5HT2AR also acts as a cellular receptor for JCV on human glial cells. Once attached, the virions enter predominantly by a ligand-inducible clathrin-dependent pathway and traffic to the ER. Inside the endoplasmic reticulum, the protein folding machinery isomerizes VP1 interpentamer disulfide bonds, thereby triggering initial uncoating. Next, the virion uses the endoplasmic reticulum-associated degradation machinery to probably translocate in the cytosol before reaching the nucleus. Nuclear entry of the viral DNA involves the selective exposure and importin recognition of VP2/Vp3 nuclear localization signal. In late phase of infection, neo-synthesized VP1 encapsulates replicated genomic DNA at nuclear domains called promyelocytic leukemia (PML) bodies, and participates in rearranging nucleosomes around the viral DNA.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Clathrin-mediated endocytosis of virus by host, Host-virus interaction, Viral attachment to host cell, Viral penetration into host cytoplasm, Virus endocytosis by host, Virus entry into host cell

Names & Taxonomyi

Protein namesi
Recommended name:
Major capsid protein VP1
Alternative name(s):
Major structural protein VP1
OrganismiJC polyomavirus (JCPyV) (JCV)
Taxonomic identifieri10632 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stagePolyomaviridae
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000008478 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host nucleus, T=7 icosahedral capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001150211 – 354Major capsid protein VP1Add BLAST354

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi97Interchain (with C-97)By similarity
Modified residuei330Phosphothreonine; by hostBy similarity1

Keywords - PTMi

Disulfide bond, Phosphoprotein

Expressioni

Keywords - Developmental stagei

Late protein

Interactioni

Subunit structurei

Homomultimer; disulfide-linked. The virus capsid is composed of 72 icosahedral units, each one composed of five disulfide-linked copies of VP1. Interacts with minor capsid proteins VP2 and VP3 (By similarity). Interacts with host 5HT2AR.By similarity2 Publications

Structurei

Secondary structure

1354
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi27 – 30Combined sources4
Helixi34 – 36Combined sources3
Beta strandi37 – 44Combined sources8
Beta strandi65 – 68Combined sources4
Helixi75 – 77Combined sources3
Beta strandi82 – 87Combined sources6
Beta strandi101 – 113Combined sources13
Helixi115 – 119Combined sources5
Beta strandi122 – 125Combined sources4
Beta strandi127 – 129Combined sources3
Beta strandi137 – 139Combined sources3
Beta strandi141 – 150Combined sources10
Beta strandi153 – 156Combined sources4
Helixi177 – 180Combined sources4
Beta strandi187 – 189Combined sources3
Turni193 – 195Combined sources3
Helixi198 – 200Combined sources3
Beta strandi201 – 203Combined sources3
Beta strandi211 – 218Combined sources8
Beta strandi226 – 232Combined sources7
Helixi248 – 250Combined sources3
Beta strandi251 – 265Combined sources15
Beta strandi270 – 274Combined sources5
Beta strandi276 – 288Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3NXDX-ray2.00A/B/C/D/E23-290[»]
3NXGX-ray1.95A/B/C/D/E23-290[»]
4JCDX-ray2.00A/B/C/D/E23-290[»]
4JCEX-ray1.90A/B/C/D/E23-290[»]
4JCFX-ray2.20A/B/C/D/E23-290[»]
4WDYX-ray1.90A/B/C/D/E23-290[»]
4WDZX-ray1.80A/B/C/D/E23-290[»]
4WE0X-ray2.10A/B/C/D/E23-290[»]
4X14X-ray2.30A/B/C/D/E23-290[»]
4X15X-ray2.11A/B/C/D/E23-290[»]
4X16X-ray1.80A/B/C/D/E23-290[»]
4X17X-ray1.75A/B/C/D/E23-290[»]
ProteinModelPortaliP03089.
SMRiP03089.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03089.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni294 – 354Intrinsically disorderedBy similarityAdd BLAST61

Domaini

The intrinsically disordered C-terminal region interacts with neighboring pentamers. The unstructured nature of this region allows to make different interactions depending on the stuctural context: pentamers present at the 12 icosahedral fivefold axes bind five pentamers, when pentamers present at the 60 icosahedral six-fold axes interacts with six pentamers (By similarity).By similarity

Sequence similaritiesi

Phylogenomic databases

KOiK19248.

Family and domain databases

Gene3Di2.60.175.10. 1 hit.
InterProiIPR000662. Capsid_VP1_Polyomavir.
IPR011222. dsDNA_vir_gr_I_capsid.
[Graphical view]
PfamiPF00718. Polyoma_coat. 1 hit.
[Graphical view]
PIRSFiPIRSF003376. Capsid_VP1_Polyomavir. 1 hit.
SUPFAMiSSF88648. SSF88648. 1 hit.

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing and alternative initiation. AlignAdd to basket

Isoform VP1 (identifier: P03089-1) [UniParc]FASTAAdd to basket
Also known as: Major capsid protein VP1

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

« Hide

        10         20         30         40         50
MAPTKRKGER KDPVQVPKLL IRGGVEVLEV KTGVDSITEV ECFLTPEMGD
60 70 80 90 100
PDEHLRGFSK SISISDTFES DSPNRDMLPC YSVARIPLPN LNEDLTCGNI
110 120 130 140 150
LMWEAVTLKT EVIGVTSLMN VHSNGQATHD NGAGKPVQGT SFHFFSVGGE
160 170 180 190 200
ALELQGVLFN YRTKYPDGTI FPKNATVQSQ VMNTEHKAYL DKNKAYPVEC
210 220 230 240 250
WVPDPTRNEN TRYFGTLTGG ENVPPVLHIT NTATTVLLDE FGVGPLCKGD
260 270 280 290 300
NLYLSAVDVC GMFTNRSGSQ QWRGLSRYFK VQLRKRRVKN PYPISFLLTD
310 320 330 340 350
LINRRTPRVD GQPMYGMDAQ VEEVRVFEGT EELPGDPDMM RYVDKYGQLQ

TKML
Note: Produced by alternative splicing of the late mRNA.
Length:354
Mass (Da):39,609
Last modified:July 21, 1986 - v1
Checksum:i33CDA3DD93026ED0
GO
Isoform VP2 (identifier: P03095-1) [UniParc]FASTAAdd to basket
Also known as: Minor capsid protein VP2
The sequence of this isoform can be found in the external entry P03095.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by alternative splicing of the late mRNA.
Length:344
Mass (Da):37,368
GO
Isoform VP3 (identifier: P03095-2) [UniParc]FASTAAdd to basket
Also known as: Minor capsid protein VP3
The sequence of this isoform can be found in the external entry P03095.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by alternative initiation at Met-120 of isoform VP2.
Length:225
Mass (Da):25,745
GO
Isoform VP4 (identifier: P03095-3) [UniParc]FASTAAdd to basket
Also known as: Viroporin VP4
The sequence of this isoform can be found in the external entry P03095.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by alternative initiation at Met-229 of isoform VP2.
Length:116
Mass (Da):12,988
GO
Isoform Agno (identifier: P03086-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P03086.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by alternative initiation of the late mRNA.
Length:71
Mass (Da):8,081
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti66D → H in strain: Isolate MAD11-BR. 1
Natural varianti74N → S in strain: Isolate NY-1B, Isolate N1 and Isolate G3. 1
Natural varianti75R → K in strain: Isolate YI, Isolate TKY-2A, Isolate MAD8-BR, Isolate HER1-BR, Isolate NY-1B, Isolate N1, Isolate N4, Isolate G3, Isolate C1, Isolate CY, Isolate MY, Isolate AIC-1A and Isolate Tokyo-1. 1
Natural varianti113I → L in strain: Isolate YI, Isolate C1, Isolate AIC-1A and Isolate Tokyo-1. 1
Natural varianti117S → T in strain: Isolate YI, Isolate TKY-2A, Isolate MAD8-BR, Isolate N4, Isolate C1, Isolate CY, Isolate MY, Isolate AIC-1A and Isolate Tokyo-1. 1
Natural varianti128T → A in strain: Isolate MAD8-BR, Isolate NY-1B, Isolate N1, Isolate G3 and Isolate N4. 1
Natural varianti158L → V in strain: Isolate YI, Isolate TKY-2A, Isolate MAD8-BR, Isolate NY-1B, Isolate N1, Isolate N4, Isolate G3, Isolate C1, Isolate CY, Isolate MY, Isolate AIC-1A and Isolate Tokyo-1. 1
Natural varianti267S → L in strain: Isolate HER1-BR. 1
Natural varianti269S → F in strain: Isolate MAD8-BR. 1
Natural varianti269S → T in strain: Isolate YI. 1
Natural varianti269S → Y in strain: Isolate TKY-2A. 1
Natural varianti321V → I in strain: Isolate C1. 1
Natural varianti345K → R in strain: Isolate YI, Isolate TKY-2A, Isolate MAD8-BR, Isolate N1, Isolate N4, Isolate G4, Isolate C1, Isolate CY, Isolate MY, Isolate AIC-1A and Isolate Tokyo-1. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02226 Genomic DNA. Translation: AAA82101.1.
D11356 Genomic DNA. Translation: BAA01958.1.
D11357 Genomic DNA. Translation: BAA01959.1.
D11358 Genomic DNA. Translation: BAA01960.1.
D11359 Genomic DNA. Translation: BAA01961.1.
D11360 Genomic DNA. Translation: BAA01962.1.
D11361 Genomic DNA. Translation: BAA01963.1.
D11362 Genomic DNA. Translation: BAA01964.1.
D11363 Genomic DNA. Translation: BAA01965.1.
D11364 Genomic DNA. Translation: BAA01966.1.
D11365 Genomic DNA. Translation: BAA01967.1.
D11366 Genomic DNA. Translation: BAA01968.1.
D11368 Genomic DNA. Translation: BAA01970.1.
D26589 Genomic DNA. Translation: BAA05636.1.
D26591 Genomic DNA. Translation: BAA05638.1.
D26592 Genomic DNA. Translation: BAA05639.1.
PIRiA03626. VVVP1J.
RefSeqiNP_043511.1. NC_001699.1. [P03089-1]

Genome annotation databases

GeneIDi1489518.
KEGGivg:1489518.

Keywords - Coding sequence diversityi

Alternative initiation, Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02226 Genomic DNA. Translation: AAA82101.1.
D11356 Genomic DNA. Translation: BAA01958.1.
D11357 Genomic DNA. Translation: BAA01959.1.
D11358 Genomic DNA. Translation: BAA01960.1.
D11359 Genomic DNA. Translation: BAA01961.1.
D11360 Genomic DNA. Translation: BAA01962.1.
D11361 Genomic DNA. Translation: BAA01963.1.
D11362 Genomic DNA. Translation: BAA01964.1.
D11363 Genomic DNA. Translation: BAA01965.1.
D11364 Genomic DNA. Translation: BAA01966.1.
D11365 Genomic DNA. Translation: BAA01967.1.
D11366 Genomic DNA. Translation: BAA01968.1.
D11368 Genomic DNA. Translation: BAA01970.1.
D26589 Genomic DNA. Translation: BAA05636.1.
D26591 Genomic DNA. Translation: BAA05638.1.
D26592 Genomic DNA. Translation: BAA05639.1.
PIRiA03626. VVVP1J.
RefSeqiNP_043511.1. NC_001699.1. [P03089-1]

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3NXDX-ray2.00A/B/C/D/E23-290[»]
3NXGX-ray1.95A/B/C/D/E23-290[»]
4JCDX-ray2.00A/B/C/D/E23-290[»]
4JCEX-ray1.90A/B/C/D/E23-290[»]
4JCFX-ray2.20A/B/C/D/E23-290[»]
4WDYX-ray1.90A/B/C/D/E23-290[»]
4WDZX-ray1.80A/B/C/D/E23-290[»]
4WE0X-ray2.10A/B/C/D/E23-290[»]
4X14X-ray2.30A/B/C/D/E23-290[»]
4X15X-ray2.11A/B/C/D/E23-290[»]
4X16X-ray1.80A/B/C/D/E23-290[»]
4X17X-ray1.75A/B/C/D/E23-290[»]
ProteinModelPortaliP03089.
SMRiP03089.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1489518.
KEGGivg:1489518.

Phylogenomic databases

KOiK19248.

Miscellaneous databases

EvolutionaryTraceiP03089.

Family and domain databases

Gene3Di2.60.175.10. 1 hit.
InterProiIPR000662. Capsid_VP1_Polyomavir.
IPR011222. dsDNA_vir_gr_I_capsid.
[Graphical view]
PfamiPF00718. Polyoma_coat. 1 hit.
[Graphical view]
PIRSFiPIRSF003376. Capsid_VP1_Polyomavir. 1 hit.
SUPFAMiSSF88648. SSF88648. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiVP1_POVJC
AccessioniPrimary (citable) accession number: P03089
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: November 30, 2016
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.