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P03087

- VP1_SV40

UniProt

P03087 - VP1_SV40

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Protein

Major capsid protein VP1

Gene
N/A
Organism
Simian virus 40 (SV40)
Status
Reviewed - 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

  1. structural molecule activity Source: InterPro

GO - Biological processi

  1. caveolin-mediated endocytosis of virus by host cell Source: UniProtKB-KW
  2. virion attachment to host cell Source: UniProtKB-KW
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 identifieri10633 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stagePolyomaviridaePolyomavirus
Virus hostiMacaca (macaques) [TaxID: 9539]
ProteomesiUP000007705: 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

  1. host cell endoplasmic reticulum Source: UniProtKB-KW
  2. host cell nucleus Source: UniProtKB-KW
  3. T=7 icosahedral viral capsid Source: UniProtKB-KW
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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi49 – 491E → A: 99% loss of infectivity ex vivo. 1 Publication
Mutagenesisi50 – 501C → S: No effect on infectivity ex vivo. 1 Publication
Mutagenesisi88 – 881C → S: 99% loss of infectivity ex vivo. 1 Publication
Mutagenesisi158 – 1581E → K or R: Complete loss of infectivity ex vivo, defective in nuclear entry. 1 Publication
Mutagenesisi161 – 1611E → K or R: 95% loss of infectivity ex vivo. 1 Publication
Mutagenesisi217 – 2171E → K or R: 99% loss of infectivity ex vivo. 1 Publication
Mutagenesisi244 – 2441V → E: Complete loss of infectivity ex vivo. 1 Publication
Mutagenesisi246 – 2461L → E: Complete loss of infectivity ex vivo. 1 Publication
Mutagenesisi255 – 2551C → S: Complete loss of infectivity ex vivo. 1 Publication
Mutagenesisi268 – 2681C → S: No effect on infectivity ex vivo. 1 Publication
Mutagenesisi331 – 3311E → K or R: Complete loss of infectivity ex vivo, defective in adsorbing to cells. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed; by host
Chaini2 – 362361Major capsid protein VP1PRO_0000115028Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi10 – 10Interchain1 Publication
Disulfide bondi105 – 105Interchain1 Publication
Disulfide bondi208 – 208Interchain1 Publication
Modified residuei338 – 3381Phosphothreonine; by host1 Publication

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 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 interactions.
MINTiMINT-238076.

Structurei

Secondary structure

1
362
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi33 – 375
Beta strandi45 – 528
Helixi61 – 633
Helixi83 – 853
Beta strandi90 – 956
Beta strandi105 – 12117
Helixi123 – 1275
Beta strandi130 – 1323
Beta strandi135 – 1373
Beta strandi145 – 1473
Beta strandi149 – 15810
Beta strandi161 – 1644
Helixi185 – 1884
Helixi192 – 1943
Beta strandi195 – 1973
Turni201 – 2033
Turni206 – 2083
Beta strandi209 – 2113
Turni213 – 2153
Beta strandi219 – 2268
Beta strandi234 – 2407
Helixi256 – 2583
Beta strandi259 – 27214
Beta strandi278 – 2825
Beta strandi285 – 29713
Beta strandi304 – 3063
Helixi324 – 3263
Beta strandi348 – 3514
Beta strandi353 – 3597

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03087.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni302 – 36261Intrinsically disorderedAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi5 – 1915Bipartite nuclear localization signalAdd
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, 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

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. Align

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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti99 – 991I → L in strain: 776.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J02400 Genomic DNA. Translation: AAB59923.1.
PIRiA31426.
E03631. VVVP14.
RefSeqiYP_003708381.1. NC_001669.1.

Genome annotation databases

GeneIDi1489530.

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:
EMBL
GenBank
DDBJ
Links Updated
J02400 Genomic DNA. Translation: AAB59923.1 .
PIRi A31426.
E03631. VVVP14.
RefSeqi YP_003708381.1. NC_001669.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1SVA X-ray 3.10 1/2/3/4/5/6 2-362 [» ]
3BWQ X-ray 2.30 A/B/C/D/E 31-298 [» ]
3BWR X-ray 2.25 A/B/C/D/E 31-298 [» ]
DisProti DP00182.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-29870N.
IntActi P03087. 3 interactions.
MINTi MINT-238076.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 1489530.

Miscellaneous databases

EvolutionaryTracei P03087.

Family and domain databases

Gene3Di 2.60.175.10. 1 hit.
InterProi IPR000662. Capsid_VP1_Polyomavir.
IPR011222. dsDNA_vir_gr_I_capsid.
[Graphical view ]
Pfami PF00718. Polyoma_coat. 1 hit.
[Graphical view ]
PIRSFi PIRSF003376. Capsid_VP1_Polyomavir. 1 hit.
SUPFAMi SSF88648. SSF88648. 1 hit.
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 776.
  3. "Correlation of the protein and nucleic acid sequences for the major structural protein of simian virus 40."
    Kempe T.D., Beattie W.G., Weissman S., Konigsberg W.
    J. Biol. Chem. 254:7561-7569(1979) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE.
  4. "An electron microscope study of the development of SV40 virus."
    Granboulan N., Tournier P., Wicker R., Bernhard W.
    J. Cell Biol. 17:423-441(1963) [PubMed] [Europe PMC] [Abstract]
    Cited for: VIRION ASSEMBLY.
  5. "Epitopes on the major capsid protein of simian virus 40."
    Babe L.M., Brew K., Matsuura S.E., Scott W.A.
    J. Biol. Chem. 264:2665-2671(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT THR-338.
  6. "Analysis of a nuclear localization signal of simian virus 40 major capsid protein Vp1."
    Ishii N., Minami N., Chen E.Y., Medina A.L., Chico M.M., Kasamatsu H.
    J. Virol. 70:1317-1322(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEAR LOCALIZATION SIGNAL.
  7. "Cys9, Cys104 and Cys207 of simian virus 40 Vp1 are essential for inter-pentamer disulfide-linkage and stabilization in cell-free lysates."
    Jao C.C., Weidman M.K., Perez A.R., Gharakhanian E.
    J. Gen. Virol. 80:2481-2489(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISULFIDE BONDS IN INTER-PENTAMER.
  8. "HSC70 interactions with SV40 viral proteins differ between permissive and nonpermissive mammalian cells."
    Sainis L., Angelidis C., Pagoulatos G.N., Lazaridis L.
    Cell Stress Chaperones 5:132-138(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HOST HSPA8.
  9. "Simian virus 40 Vp1 DNA-binding domain is functionally separable from the overlapping nuclear localization signal and is required for effective virion formation and full viability."
    Li P.P., Nakanishi A., Shum D., Sun P.C., Salazar A.M., Fernandez C.F., Chan S.W., Kasamatsu H.
    J. Virol. 75:7321-7329(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: DNA-BINDING, NUCLEAR LOCALIZATION SIGNAL.
  10. "Cellular transcription factor Sp1 recruits simian virus 40 capsid proteins to the viral packaging signal, ses."
    Gordon-Shaag A., Ben-Nun-Shaul O., Roitman V., Yosef Y., Oppenheim A.
    J. Virol. 76:5915-5924(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HOST SP1.
  11. "Importance of Vp1 calcium-binding residues in assembly, cell entry, and nuclear entry of simian virus 40."
    Li P.P., Naknanishi A., Tran M.A., Ishizu K., Kawano M., Phillips M., Handa H., Liddington R.C., Kasamatsu H.
    J. Virol. 77:7527-7538(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF GLU-49; GLU-217 AND GLU-331.
  12. "Cys254 and Cys49/Cys87of simian virus 40 Vp1 are essential in formation of infectious virions."
    Gharakhanian E., Mana W., Norng M.
    Virus Res. 107:21-25(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF CYS-50; CYS-88; CYS-255 AND CYS-268.
  13. "Identification of amino acid residues within simian virus 40 capsid proteins Vp1, Vp2, and Vp3 that are required for their interaction and for viral infection."
    Nakanishi A., Nakamura A., Liddington R., Kasamatsu H.
    J. Virol. 80:8891-8898(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH VP2 AND VP3, MUTAGENESIS OF VAL-244 AND LEU-246.
  14. "Importance of calcium-binding site 2 in simian virus 40 infection."
    Li P.P., Nguyen A.P., Qu Q., Jafri Q.H., Aungsumart S., Cheng R.H., Kasamatsu H.
    J. Virol. 81:6099-6105(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF GLU-158 AND GLU-161.
  15. "Simian Virus 40 depends on ER protein folding and quality control factors for entry into host cells."
    Schelhaas M., Malmstroem J., Pelkmans L., Haugstetter J., Ellgaard L., Gruenewald K., Helenius A.
    Cell 131:516-529(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: ISOMERIZATION OF DISULFIDE BONDS.
  16. "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.
  17. Cited for: X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS).
  18. "The structure of simian virus 40 refined at 3.1-A resolution."
    Stehle T., Gamblin S.J., Yan Y., Harrison S.C.
    Structure 4:165-182(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF 2-362.
  19. "Structural basis of GM1 ganglioside recognition by simian virus 40."
    Neu U., Woellner K., Gauglitz G., Stehle T.
    Proc. Natl. Acad. Sci. U.S.A. 105:5219-5224(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF 31-298.

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: October 29, 2014
This is version 116 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

External Data

Dasty 3