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Protein

Major capsid protein VP1

Gene
N/A
Organism
Simian virus 40 (SV40)
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. Binds to N-glycolylneuraminic analog of the ganglioside GM1 on the cell surface to provide virion attachment to target cell. 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. The assembly takes place in the cell nucleus. Encapsulates the genomic DNA and participates in rearranging nucleosomes around the viral DNA. The viral progenies exit the cells by lytic release.

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:
Major capsid protein VP1
Alternative name(s):
Major structural protein VP1
OrganismiSimian virus 40 (SV40)
Taxonomic identifieri1891767 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stagePolyomaviridae
Virus hostiMacaca (macaques) [TaxID: 9539]
Proteomesi
  • UP000007705 Componenti: Genome

Subcellular locationi

  • Virion
  • Host nucleus
  • Host endoplasmic reticulum

  • Note: Following host cell entry, the virion enters into the endoplasmic reticulum through a calveolar-dependent pathway. Then, viral DNA is translocated to the nucleus. Shortly after synthesis, a nuclear localization signal directs VP1 to the cell nucleus where virion assembly occurs.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi49E → A: 99% loss of infectivity ex vivo. 1 Publication1
Mutagenesisi50C → S: No effect on infectivity ex vivo. 1 Publication1
Mutagenesisi88C → S: 99% loss of infectivity ex vivo. 1 Publication1
Mutagenesisi158E → K or R: Complete loss of infectivity ex vivo, defective in nuclear entry. 1 Publication1
Mutagenesisi161E → K or R: 95% loss of infectivity ex vivo. 1 Publication1
Mutagenesisi217E → K or R: 99% loss of infectivity ex vivo. 1 Publication1
Mutagenesisi244V → E: Complete loss of infectivity ex vivo. 1 Publication1
Mutagenesisi246L → E: Complete loss of infectivity ex vivo. 1 Publication1
Mutagenesisi255C → S: Complete loss of infectivity ex vivo. 1 Publication1
Mutagenesisi268C → S: No effect on infectivity ex vivo. 1 Publication1
Mutagenesisi331E → K or R: Complete loss of infectivity ex vivo, defective in adsorbing to cells. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by host
ChainiPRO_00001150282 – 362Major capsid protein VP1Add BLAST361

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi10Interchain1 Publication
Disulfide bondi105Interchain1 Publication
Disulfide bondi208Interchain1 Publication
Modified residuei338Phosphothreonine; by host1 Publication1

Keywords - PTMi

Disulfide bond, Phosphoprotein

PTM databases

iPTMnetiP03087.

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 agnoprotein (By similarity). Interacts with minor capsid proteins VP2 and VP3. Interacts with host HSPA8; this interaction probably participates in virus assembly. Interacts with host SP1; this interaction enhances the efficiency of viral packaging.By similarity4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
P030933EBI-1555770,EBI-1555798
Parp1P111032EBI-1555770,EBI-642213From a different organism.
vp3O928373EBI-1555770,EBI-7196689

Protein-protein interaction databases

DIPiDIP-29870N.
IntActiP03087. 3 interactors.
MINTiMINT-238076.

Structurei

Secondary structure

1362
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi33 – 37Combined sources5
Beta strandi45 – 52Combined sources8
Helixi61 – 63Combined sources3
Helixi83 – 85Combined sources3
Beta strandi90 – 95Combined sources6
Beta strandi105 – 121Combined sources17
Helixi123 – 127Combined sources5
Beta strandi130 – 132Combined sources3
Beta strandi135 – 137Combined sources3
Beta strandi145 – 147Combined sources3
Beta strandi149 – 158Combined sources10
Beta strandi161 – 164Combined sources4
Helixi185 – 188Combined sources4
Helixi192 – 194Combined sources3
Beta strandi195 – 197Combined sources3
Turni201 – 203Combined sources3
Turni206 – 208Combined sources3
Beta strandi209 – 211Combined sources3
Turni213 – 215Combined sources3
Beta strandi219 – 226Combined sources8
Beta strandi234 – 240Combined sources7
Helixi256 – 258Combined sources3
Beta strandi259 – 272Combined sources14
Beta strandi278 – 282Combined sources5
Beta strandi285 – 297Combined sources13
Beta strandi304 – 306Combined sources3
Helixi324 – 326Combined sources3
Beta strandi348 – 351Combined sources4
Beta strandi353 – 359Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SVAX-ray3.101/2/3/4/5/62-362[»]
3BWQX-ray2.30A/B/C/D/E31-298[»]
3BWRX-ray2.25A/B/C/D/E31-298[»]
DisProtiDP00182.
SMRiP03087.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03087.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni302 – 362Intrinsically disorderedAdd BLAST61

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi5 – 19Bipartite nuclear localization signalAdd BLAST15

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, whereas pentamers present at the 60 icosahedral six-fold axes interact with six pentamers.
A DNA-binding domain overlapping a bipartite nuclear localization signal is present in the N-terminal region of the protein and is required for efficient virus formation.

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.

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

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

Isoform VP1 (identifier: P03087-1) [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
MAPTKRKGSC PGAAPKKPKE PVQVPKLVIK GGIEVLGVKT GVDSFTEVEC
60 70 80 90 100
FLNPQMGNPD EHQKGLSKSL AAEKQFTDDS PDKEQLPCYS VARIPLPNIN
110 120 130 140 150
EDLTCGNILM WEAVTVKTEV IGVTAMLNLH SGTQKTHENG AGKPIQGSNF
160 170 180 190 200
HFFAVGGEPL ELQGVLANYR TKYPAQTVTP KNATVDSQQM NTDHKAVLDK
210 220 230 240 250
DNAYPVECWV PDPSKNENTR YFGTYTGGEN VPPVLHITNT ATTVLLDEQG
260 270 280 290 300
VGPLCKADSL YVSAVDICGL FTNTSGTQQW KGLPRYFKIT LRKRSVKNPY
310 320 330 340 350
PISFLLSDLI NRRTQRVDGQ PMIGMSSQVE EVRVYEDTEE LPGDPDMIRY
360
IDEFGQTTTR MQ
Note: Produced by alternative splicing of the late mRNA (16s mRNA).
Length:362
Mass (Da):39,906
Last modified:November 25, 2008 - v2
Checksum:i81C28EB7EA51D398
GO
Isoform VP2 (identifier: P03093-1) [UniParc]FASTAAdd to basket
Also known as: Minor capsid protein VP2
The sequence of this isoform can be found in the external entry P03093.
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 (19s mRNA).
Length:352
Mass (Da):38,539
GO
Isoform VP3 (identifier: P03093-2) [UniParc]FASTAAdd to basket
Also known as: Minor capsid protein VP3
The sequence of this isoform can be found in the external entry P03093.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by alternative initiation at Met-119 of isoform VP2.
Length:234
Mass (Da):26,963
GO
Isoform VP4 (identifier: P03093-3) [UniParc]FASTAAdd to basket
Also known as: Viroporin VP4
The sequence of this isoform can be found in the external entry P03093.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by alternative initiation at Met-228 of isoform VP2.
Length:125
Mass (Da):13,922
GO
Isoform Agno (identifier: P03084-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry P03084.
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 (16s and 19s mRNAs).
Length:62
Mass (Da):7,336
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti99I → L in strain: 776. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02400 Genomic DNA. Translation: AAB59923.1.
PIRiA31426.
E03631. VVVP14.
RefSeqiYP_003708381.1. NC_001669.1.

Genome annotation databases

GeneIDi29031018.
KEGGivg:1489530.

Keywords - Coding sequence diversityi

Alternative initiation, Alternative splicing

Cross-referencesi

Web resourcesi

Virus Particle ExploreR db

Icosahedral capsid structure

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02400 Genomic DNA. Translation: AAB59923.1.
PIRiA31426.
E03631. VVVP14.
RefSeqiYP_003708381.1. NC_001669.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SVAX-ray3.101/2/3/4/5/62-362[»]
3BWQX-ray2.30A/B/C/D/E31-298[»]
3BWRX-ray2.25A/B/C/D/E31-298[»]
DisProtiDP00182.
SMRiP03087.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-29870N.
IntActiP03087. 3 interactors.
MINTiMINT-238076.

PTM databases

iPTMnetiP03087.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi29031018.
KEGGivg:1489530.

Phylogenomic databases

KOiK19248.

Miscellaneous databases

EvolutionaryTraceiP03087.

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_SV40
AccessioniPrimary (citable) accession number: P03087
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: November 25, 2008
Last modified: November 30, 2016
This is version 126 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, Complete proteome, Direct protein sequencing, 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.