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P03087 (VP1_SV40) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 114. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Major capsid protein VP1
Alternative name(s):
Major structural protein VP1
OrganismSimian virus 40 (SV40) [Reference proteome]
Taxonomic identifier10633 [NCBI]
Taxonomic lineageVirusesdsDNA viruses, no RNA stagePolyomaviridaePolyomavirus
Virus hostMacaca (macaques) [TaxID: 9539]

Protein attributes

Sequence length362 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subunit structure

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. Ref.7 Ref.8 Ref.10 Ref.13 Ref.15

Subcellular location

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.

Domain

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 similarities

Belongs to the polyomaviruses coat protein VP1 family.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

P030933EBI-1555770,EBI-1555798
Parp1P111032EBI-1555770,EBI-642213From a different organism.
vp3O928373EBI-1555770,EBI-7196689

Alternative products

This entry describes 5 isoforms produced by alternative splicing and alternative initiation. [Align] [Select]
Isoform VP1 (identifier: P03087-1)

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.
Note: Produced by alternative splicing of the late mRNA (16s mRNA).
Isoform VP2 (identifier: P03093-1)

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).
Isoform VP3 (identifier: P03093-2)

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.
Isoform VP4 (identifier: P03093-3)

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.
Isoform Agno (identifier: P03084-1)

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).

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed; by host
Chain2 – 362361Major capsid protein VP1
PRO_0000115028

Regions

Region302 – 36261Intrinsically disordered
Motif5 – 1915Bipartite nuclear localization signal

Amino acid modifications

Modified residue3381Phosphothreonine; by host Ref.5
Disulfide bond10Interchain Ref.7 Ref.15
Disulfide bond105Interchain Ref.7 Ref.15
Disulfide bond208Interchain Ref.7 Ref.15

Natural variations

Natural variant991I → L in strain: 776.

Experimental info

Mutagenesis491E → A: 99% loss of infectivity ex vivo. Ref.11
Mutagenesis501C → S: No effect on infectivity ex vivo. Ref.12
Mutagenesis881C → S: 99% loss of infectivity ex vivo. Ref.12
Mutagenesis1581E → K or R: Complete loss of infectivity ex vivo, defective in nuclear entry. Ref.14
Mutagenesis1611E → K or R: 95% loss of infectivity ex vivo. Ref.14
Mutagenesis2171E → K or R: 99% loss of infectivity ex vivo. Ref.11
Mutagenesis2441V → E: Complete loss of infectivity ex vivo. Ref.13
Mutagenesis2461L → E: Complete loss of infectivity ex vivo. Ref.13
Mutagenesis2551C → S: Complete loss of infectivity ex vivo. Ref.12
Mutagenesis2681C → S: No effect on infectivity ex vivo. Ref.12
Mutagenesis3311E → K or R: Complete loss of infectivity ex vivo, defective in adsorbing to cells. Ref.11

Secondary structure

........................................................ 362
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform VP1 (Major capsid protein VP1) [UniParc].

Last modified November 25, 2008. Version 2.
Checksum: 81C28EB7EA51D398

FASTA36239,906
        10         20         30         40         50         60 
MAPTKRKGSC PGAAPKKPKE PVQVPKLVIK GGIEVLGVKT GVDSFTEVEC FLNPQMGNPD 

        70         80         90        100        110        120 
EHQKGLSKSL AAEKQFTDDS PDKEQLPCYS VARIPLPNIN EDLTCGNILM WEAVTVKTEV 

       130        140        150        160        170        180 
IGVTAMLNLH SGTQKTHENG AGKPIQGSNF HFFAVGGEPL ELQGVLANYR TKYPAQTVTP 

       190        200        210        220        230        240 
KNATVDSQQM NTDHKAVLDK DNAYPVECWV PDPSKNENTR YFGTYTGGEN VPPVLHITNT 

       250        260        270        280        290        300 
ATTVLLDEQG VGPLCKADSL YVSAVDICGL FTNTSGTQQW KGLPRYFKIT LRKRSVKNPY 

       310        320        330        340        350        360 
PISFLLSDLI NRRTQRVDGQ PMIGMSSQVE EVRVYEDTEE LPGDPDMIRY IDEFGQTTTR 


MQ 

« Hide

Isoform VP2 (Minor capsid protein VP2) [UniParc].

See P03093.

Isoform VP3 (Minor capsid protein VP3) [UniParc].

See P03093.

Isoform VP4 (Viroporin VP4) [UniParc].

See P03093.

Isoform Agno [UniParc].

See P03084.

References

[1]"The genome of simian virus 40."
Reddy V.B., Thimmappaya B., Dhar R., Subramanian K.N., Zain B.S., Pan J., Ghosh P.K., Celma M.L., Weissman S.M.
Science 200:494-502(1978) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Complete nucleotide sequence of SV40 DNA."
Fiers W., Contreras R., Haegeman G., Rogiers R., van de Voorde A., van Heuverswyn H., van Herreweghe J., Volckaert G., Ysebaert M.
Nature 273:113-120(1978) [PubMed] [Europe PMC] [Abstract]
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]"Structure of simian virus 40 at 3.8-A resolution."
Liddinngton R.C., Yan Y., Moulai J., Sahli R., Benjamin T.L., Harrison S.C.
Nature 354:278-284(1991) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J02400 Genomic DNA. Translation: AAB59923.1.
PIRA31426.
VVVP14. E03631.
RefSeqYP_003708381.1. NC_001669.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
DisProtDP00182.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-29870N.
IntActP03087. 3 interactions.
MINTMINT-238076.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID1489530.

Family and domain databases

Gene3D2.60.175.10. 1 hit.
InterProIPR000662. Capsid_VP1_Polyomavir.
IPR011222. dsDNA_vir_gr_I_capsid.
[Graphical view]
PfamPF00718. Polyoma_coat. 1 hit.
[Graphical view]
PIRSFPIRSF003376. Capsid_VP1_Polyomavir. 1 hit.
SUPFAMSSF88648. SSF88648. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP03087.

Entry information

Entry nameVP1_SV40
AccessionPrimary (citable) accession number: P03087
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: November 25, 2008
Last modified: July 9, 2014
This is version 114 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references