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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 stagePolyomaviridae
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)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by host
ChainiPRO_00001150252 – 384Capsid protein VP1Add BLAST383

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi12InterchainBy similarity
Disulfide bondi115InterchainBy similarity
Modified residuei358Phosphothreonine; 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).By similarity

Structurei

Secondary structure

1384
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi36 – 40Combined sources5
Beta strandi47 – 54Combined sources8
Beta strandi58 – 60Combined sources3
Turni67 – 70Combined sources4
Helixi71 – 73Combined sources3
Helixi93 – 95Combined sources3
Beta strandi100 – 105Combined sources6
Beta strandi118 – 130Combined sources13
Helixi133 – 137Combined sources5
Beta strandi141 – 143Combined sources3
Beta strandi145 – 147Combined sources3
Turni148 – 151Combined sources4
Beta strandi152 – 155Combined sources4
Beta strandi162 – 171Combined sources10
Beta strandi174 – 177Combined sources4
Beta strandi188 – 191Combined sources4
Helixi194 – 198Combined sources5
Helixi204 – 207Combined sources4
Beta strandi214 – 216Combined sources3
Turni225 – 227Combined sources3
Beta strandi228 – 230Combined sources3
Beta strandi238 – 245Combined sources8
Beta strandi253 – 259Combined sources7
Helixi275 – 277Combined sources3
Beta strandi278 – 291Combined sources14
Beta strandi298 – 302Combined sources5
Beta strandi305 – 317Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP49302.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni322 – 384Intrinsically disorderedBy similarityAdd BLAST63

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
PDB 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.
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...

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: November 2, 2016
This is version 100 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.