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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 stagePolyomaviridaePolyomavirus
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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 354354Major capsid protein VP1PRO_0000115021Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi97 – 97Interchain (with C-97)By similarity
Modified residuei330 – 3301Phosphothreonine; by hostBy similarity

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

1
354
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi27 – 304Combined sources
Helixi34 – 363Combined sources
Beta strandi37 – 448Combined sources
Beta strandi65 – 684Combined sources
Helixi75 – 773Combined sources
Beta strandi82 – 876Combined sources
Beta strandi101 – 11313Combined sources
Helixi115 – 1195Combined sources
Beta strandi122 – 1254Combined sources
Beta strandi127 – 1293Combined sources
Beta strandi137 – 1393Combined sources
Beta strandi141 – 15010Combined sources
Beta strandi153 – 1564Combined sources
Helixi177 – 1804Combined sources
Beta strandi187 – 1893Combined sources
Turni193 – 1953Combined sources
Helixi198 – 2003Combined sources
Beta strandi201 – 2033Combined sources
Beta strandi211 – 2188Combined sources
Beta strandi226 – 2327Combined sources
Helixi248 – 2503Combined sources
Beta strandi251 – 26515Combined sources
Beta strandi270 – 2745Combined sources
Beta strandi276 – 28813Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 11-353.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03089.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni294 – 35461Intrinsically disorderedBy similarityAdd
BLAST

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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti66 – 661D → H in strain: Isolate MAD11-BR.
Natural varianti74 – 741N → S in strain: Isolate NY-1B, Isolate N1 and Isolate G3.
Natural varianti75 – 751R → 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.
Natural varianti113 – 1131I → L in strain: Isolate YI, Isolate C1, Isolate AIC-1A and Isolate Tokyo-1.
Natural varianti117 – 1171S → 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.
Natural varianti128 – 1281T → A in strain: Isolate MAD8-BR, Isolate NY-1B, Isolate N1, Isolate G3 and Isolate N4.
Natural varianti158 – 1581L → 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.
Natural varianti267 – 2671S → L in strain: Isolate HER1-BR.
Natural varianti269 – 2691S → F in strain: Isolate MAD8-BR.
Natural varianti269 – 2691S → T in strain: Isolate YI.
Natural varianti269 – 2691S → Y in strain: Isolate TKY-2A.
Natural varianti321 – 3211V → I in strain: Isolate C1.
Natural varianti345 – 3451K → 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.

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
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. Positions 11-353.
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...

Publicationsi

  1. "Human polyomavirus JC virus genome."
    Frisque R.J., Bream G.L., Cannella M.T.
    J. Virol. 51:458-469(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: MAD-1.
  2. "Origin of JC polyomavirus variants associated with progressive multifocal leukoencephalopathy."
    Iida T., Kitamura T., Guo J., Taguchi F., Aso Y., Nagashima K., Yogo Y.
    Proc. Natl. Acad. Sci. U.S.A. 90:5062-5065(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: C1, CY, G2, G3, HER1-BR, MAD11-BR, MAD8-BR, MY, N1, N4, NY-1B and Tokyo-1.
  3. "Occurrence of multiple JC virus variants with distinctive regulatory sequences in the brain of a single patient with progressive multifocal leukoencephalopathy."
    Yogo Y., Guo J., Iida T., Satoh K.I., Taguchi F., Takahashi H., Hall W.W., Nagashima K.
    Virus Genes 8:99-105(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: NY-1B.
  4. "Phylogenetic comparison between archetypal and disease-associated JC virus isolates in Japan."
    Kato K., Guo J., Taguchi F., Daimaru O., Tajima T., Haibara H., Matsuda J., Sumiya S., Yogo Y.
    Jpn. J. Med. Sci. Biol. 47:167-178(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: AIC-1A, TKY-2A and YI.
  5. "Infection of glial cells by the human polyomavirus JC is mediated by an N-linked glycoprotein containing terminal alpha(2-6)-linked sialic acids."
    Liu C.K., Wei G., Atwood W.J.
    J. Virol. 72:4643-4649(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: VIRION ENTRY.
  6. "JC virus enters human glial cells by clathrin-dependent receptor-mediated endocytosis."
    Pho M.T., Ashok A., Atwood W.J.
    J. Virol. 74:2288-2292(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "Nuclear entry mechanism of the human polyomavirus JC virus-like particle: role of importins and the nuclear pore complex."
    Qu Q., Sawa H., Suzuki T., Semba S., Henmi C., Okada Y., Tsuda M., Tanaka S., Atwood W.J., Nagashima K.
    J. Biol. Chem. 279:27735-27742(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEAR SIGNAL.
  8. Cited for: INTERACTION WITH HOST 5HT2AR.
  9. "Structure, attachment and entry of polyoma- and papillomaviruses."
    Sapp M., Day P.M.
    Virology 384:400-409(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  10. "Major and minor capsid proteins of human polyomavirus JC cooperatively accumulate to nuclear domain 10 for assembly into virions."
    Shishido-Hara Y., Ichinose S., Higuchi K., Hara Y., Yasui K.
    J. Virol. 78:9890-9903(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: ASSEMBLY AT PML NUCLEAR BODIES.
  11. "The Polyomaviridae: Contributions of virus structure to our understanding of virus receptors and infectious entry."
    Neu U., Stehle T., Atwood W.J.
    Virology 384:389-399(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  12. "Structure-function analysis of the human JC polyomavirus establishes the LSTc pentasaccharide as a functional receptor motif."
    Neu U., Maginnis M.S., Palma A.S., Stroeh L.J., Nelson C.D., Feizi T., Atwood W.J., Stehle T.
    Cell Host Microbe 8:309-319(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 23-290 IN COMPLEX WITH LINEAR SIALYLATED PENTASACCHARIDE.

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: October 14, 2015
This is version 96 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

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.