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P03087

- VP1_SV40

UniProt

P03087 - VP1_SV40

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
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    • History
      Entry version 115 (01 Oct 2014)
      Sequence version 2 (25 Nov 2008)
      Previous versions | rss
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    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. protein binding Source: IntAct
    2. 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

    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-SubCell
    2. host cell nucleus Source: UniProtKB-SubCell
    3. T=7 icosahedral viral capsid Source: UniProtKB-KW

    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

    MAPTKRKGSC PGAAPKKPKE PVQVPKLVIK GGIEVLGVKT GVDSFTEVEC    50
    FLNPQMGNPD EHQKGLSKSL AAEKQFTDDS PDKEQLPCYS VARIPLPNIN 100
    EDLTCGNILM WEAVTVKTEV IGVTAMLNLH SGTQKTHENG AGKPIQGSNF 150
    HFFAVGGEPL ELQGVLANYR TKYPAQTVTP KNATVDSQQM NTDHKAVLDK 200
    DNAYPVECWV PDPSKNENTR YFGTYTGGEN VPPVLHITNT ATTVLLDEQG 250
    VGPLCKADSL YVSAVDICGL FTNTSGTQQW KGLPRYFKIT LRKRSVKNPY 300
    PISFLLSDLI NRRTQRVDGQ PMIGMSSQVE EVRVYEDTEE LPGDPDMIRY 350
    IDEFGQTTTR MQ 362

    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 1, 2014
    This is version 115 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