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Protein

Capsid protein VP1

Gene
N/A
Organism
Murine polyomavirus (strain P16 small-plaque) (MPyV)
Status
Reviewed-Annotation score: Annotation score: 3 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 terminal alpha(2,3)-linked sialic acids on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through caveolin-mediated endocytosis. Once attached, the virion is internalized by caveolin-mediated endocytosis and traffics to the endoplasmic reticulum. 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 in the nucleus, and participates in rearranging nucleosomes around the viral DNA (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Caveolin-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:
Capsid protein VP1
OrganismiMurine polyomavirus (strain P16 small-plaque) (MPyV)
Taxonomic identifieri47935 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stagePolyomaviridaePolyomavirus
Virus hostiMus musculus (Mouse) [TaxID: 10090]

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
Initiator methionineiRemoved; by host
Chaini2 – 384383Capsid protein VP1PRO_0000115025Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi12 – 12InterchainBy similarity
Disulfide bondi115 – 115InterchainBy similarity
Modified residuei358 – 3581Phosphothreonine; 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).By similarity

Structurei

Secondary structure

1
384
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi36 – 405Combined sources
Beta strandi47 – 548Combined sources
Beta strandi58 – 603Combined sources
Turni67 – 704Combined sources
Helixi71 – 733Combined sources
Helixi93 – 953Combined sources
Beta strandi100 – 1056Combined sources
Beta strandi118 – 13013Combined sources
Helixi133 – 1375Combined sources
Beta strandi141 – 1433Combined sources
Beta strandi145 – 1473Combined sources
Turni148 – 1514Combined sources
Beta strandi152 – 1554Combined sources
Beta strandi162 – 17110Combined sources
Beta strandi174 – 1774Combined sources
Beta strandi188 – 1914Combined sources
Helixi194 – 1985Combined sources
Helixi204 – 2074Combined sources
Beta strandi214 – 2163Combined sources
Turni225 – 2273Combined sources
Beta strandi228 – 2303Combined sources
Beta strandi238 – 2458Combined sources
Beta strandi253 – 2597Combined sources
Helixi275 – 2773Combined sources
Beta strandi278 – 29114Combined sources
Beta strandi298 – 3025Combined sources
Beta strandi305 – 31713Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CN3X-ray2.20A/B/C/D/E35-317[»]
1SIDX-ray3.65A/B/C/D/E/F2-384[»]
1SIEX-ray3.65A/B/C/D/E/F2-384[»]
1VPNX-ray2.00A/B/C/D/E33-321[»]
1VPSX-ray1.90A/B/C/D/E33-321[»]
5CPUX-ray1.64A/B/C/D/E34-317[»]
5CPWX-ray1.75A/B/C/D/E34-317[»]
5CPXX-ray1.87A/B/C/D/E34-317[»]
5CPYX-ray1.93A/B/C/D/E34-317[»]
5CPZX-ray1.71A/B/C/D/E34-317[»]
5CQ0X-ray1.90A/B/C/D/E34-317[»]
ProteinModelPortaliP49302.
SMRiP49302. Positions 18-384.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP49302.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni322 – 38463Intrinsically 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.

Sequence similaritiesi

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.

Sequencei

Sequence statusi: Complete.

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

P49302-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAPKRKSGVS KCETKCTKAC PRPAPVPKLL IKGGMEVLDL VTGPDSVTEI
60 70 80 90 100
EAFLNPRMGQ PPTPESLTEG GQYYGWSRGI NLATSDTEDS PGNNTLPTWS
110 120 130 140 150
MAKLQLPMLN EDLTCDTLQM WEAVSVKTEV VGSGSLLDVH GFNKPTDTVN
160 170 180 190 200
TKGISTPVEG SQYHVFAVGG EPLDLQGLVT DARTKYKEEG VVTIKTITKK
210 220 230 240 250
DMVNKDQVLN PISKAKLDKD GMYPVEIWHP DPAKNENTRY FGNYTGGTTT
260 270 280 290 300
PPVLQFTNTL TTVLLDENGV GPLCKGEGLY LSCVDIMGWR VTRNYDVHHW
310 320 330 340 350
RGLPRYFKIT LRKRWVKNPY PMASLISSLF NNMLPQVQGQ PMEGENTQVE
360 370 380
EVRVYDGTEP VPGDPDMTRY VDRFGKTKTV FPGN
Length:384
Mass (Da):42,505
Last modified:January 23, 2007 - v2
Checksum:i324AACBB94BAA63B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M34958 Genomic DNA. Translation: AAA46561.1.

Cross-referencesi

Web resourcesi

Virus Particle ExploreR db

Icosahedral capsid structure in complex with 3'sialyl lactose

Virus Particle ExploreR db

Icosahedral capsid structure in complex with a disialylated oligosaccharide

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M34958 Genomic DNA. Translation: AAA46561.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CN3X-ray2.20A/B/C/D/E35-317[»]
1SIDX-ray3.65A/B/C/D/E/F2-384[»]
1SIEX-ray3.65A/B/C/D/E/F2-384[»]
1VPNX-ray2.00A/B/C/D/E33-321[»]
1VPSX-ray1.90A/B/C/D/E33-321[»]
5CPUX-ray1.64A/B/C/D/E34-317[»]
5CPWX-ray1.75A/B/C/D/E34-317[»]
5CPXX-ray1.87A/B/C/D/E34-317[»]
5CPYX-ray1.93A/B/C/D/E34-317[»]
5CPZX-ray1.71A/B/C/D/E34-317[»]
5CQ0X-ray1.90A/B/C/D/E34-317[»]
ProteinModelPortaliP49302.
SMRiP49302. Positions 18-384.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP49302.

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. "A single-amino-acid substitution in polyomavirus VP1 correlates with plaque size and hemagglutination behavior."
    Freund R., Garcea R.L., Sahli R., Benjamin T.L.
    J. Virol. 65:350-355(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "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.
  3. "Structure of murine polyomavirus complexed with an oligosaccharide receptor fragment."
    Stehle T., Yan Y., Benjamin T.L., Harrison S.C.
    Nature 369:160-163(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.65 ANGSTROMS).
  4. "Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments."
    Stehle T., Harrison S.C.
    Structure 4:183-194(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.65 ANGSTROMS).
  5. "High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding."
    Stehle T., Harrison S.C.
    EMBO J. 16:5139-5148(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).

Entry informationi

Entry nameiVP1_POVMP
AccessioniPrimary (citable) accession number: P49302
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: January 23, 2007
Last modified: April 13, 2016
This is version 98 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

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.