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P03136

- CAPSD_PAVHH

UniProt

P03136 - CAPSD_PAVHH

Protein

Capsid protein VP1

Gene
N/A
Organism
Hamster parvovirus H1
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 74 (01 Oct 2014)
      Sequence version 2 (05 Apr 2011)
      Previous versions | rss
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    Functioni

    Capsid protein self-assembles to form an icosahedral capsid with a T=1 symmetry, about 22 nm in diameter, and consisting of 60 copies of two size variants of the capsid proteins, VP1 and VP2, which differ by the presence of an N-terminal extension in the minor protein VP1. The capsid encapsulates the genomic ssDNA. Capsid proteins are responsible for the attachment to host cell receptors. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptors also induces capsid rearrangements leading to surface exposure of VP1 N-terminus, specifically its phospholipase A2-like region and putative nuclear localization signal(s). VP1 N-terminus might serve as a lipolytic enzyme to breach the endosomal membrane during entry into host cell and might contribute to virus transport to the nucleus By similarity.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi328 – 3281Magnesium 1By similarity

    GO - Molecular functioni

    1. metal ion binding Source: UniProtKB-KW
    2. structural molecule activity Source: InterPro

    GO - Biological processi

    1. clathrin-mediated endocytosis of virus by host cell Source: UniProtKB-KW
    2. microtubule-dependent intracellular transport of viral material towards nucleus Source: UniProtKB-KW
    3. permeabilization of host organelle membrane involved in viral entry into host cell Source: UniProtKB-KW
    4. viral penetration into host nucleus Source: UniProtKB-KW
    5. virion attachment to host cell Source: UniProtKB-KW

    Keywords - Biological processi

    Clathrin-mediated endocytosis of virus by host, Cytoplasmic inwards viral transport, Host-virus interaction, Microtubular inwards viral transport, Viral attachment to host cell, Viral penetration into host cytoplasm, Viral penetration into host nucleus, Viral penetration via permeabilization of host membrane, Virus endocytosis by host, Virus entry into host cell

    Keywords - Ligandi

    Magnesium, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Capsid protein VP1
    Alternative name(s):
    Coat protein VP1
    OrganismiHamster parvovirus H1
    Taxonomic identifieri10799 [NCBI]
    Taxonomic lineageiVirusesssDNA virusesParvoviridaeParvovirinaeProtoparvovirus
    Virus hostiCricetidae sp. (Hamster) [TaxID: 36483]
    Rattus norvegicus (Rat) [TaxID: 10116]
    ProteomesiUP000007897: Genome

    Subcellular locationi

    Virion By similarity. Host nucleus Curated

    GO - Cellular componenti

    1. host cell nucleus Source: UniProtKB-SubCell
    2. intracellular Source: GOC
    3. T=1 icosahedral viral capsid Source: UniProtKB-KW

    Keywords - Cellular componenti

    Capsid protein, Host nucleus, T=1 icosahedral capsid protein, Virion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 734734Capsid protein VP1PRO_0000039431Add
    BLAST

    Structurei

    Secondary structure

    1
    734
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi192 – 1987
    Beta strandi201 – 21515
    Beta strandi218 – 2214
    Beta strandi223 – 2275
    Beta strandi232 – 2354
    Beta strandi237 – 2393
    Helixi243 – 2453
    Beta strandi248 – 25710
    Helixi263 – 2664
    Helixi269 – 27810
    Beta strandi279 – 30123
    Beta strandi311 – 3155
    Beta strandi321 – 3255
    Helixi336 – 3394
    Beta strandi354 – 3607
    Beta strandi364 – 3663
    Beta strandi381 – 3833
    Helixi388 – 3903
    Helixi396 – 3994
    Beta strandi403 – 4053
    Beta strandi426 – 4283
    Helixi432 – 4343
    Beta strandi441 – 4433
    Turni457 – 4593
    Turni474 – 4763
    Beta strandi480 – 4845
    Beta strandi492 – 4954
    Beta strandi498 – 5014
    Turni510 – 5134
    Helixi516 – 5183
    Beta strandi521 – 5255
    Helixi527 – 5293
    Beta strandi541 – 5455
    Beta strandi550 – 5523
    Helixi556 – 5583
    Beta strandi560 – 5623
    Helixi572 – 5743
    Beta strandi575 – 5806
    Helixi590 – 5923
    Turni610 – 6123
    Beta strandi622 – 6243
    Beta strandi633 – 6353
    Beta strandi644 – 6485
    Beta strandi668 – 68417
    Helixi708 – 7114
    Beta strandi729 – 7313

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4G0RX-ray2.70A1-734[»]
    4GBTX-ray3.20A1-734[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni19 – 6446Phospholipase A2-likeBy similarityAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi4 – 1310Nuclear localization signalSequence Analysis

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi166 – 18217Gly-richAdd
    BLAST

    Domaini

    The N-terminus of VP1 is sequestered within the mature capsid. It contains a phospholipase A2-like region and putative nuclear localization signals.

    Sequence similaritiesi

    Belongs to the parvoviridae capsid protein family.Curated

    Family and domain databases

    Gene3Di2.170.30.10. 1 hit.
    InterProiIPR016184. Capsid/spike_ssDNA_virus.
    IPR001403. Parvovirus_coat.
    IPR013607. Parvovirus_coat_VP1_N.
    [Graphical view]
    PfamiPF00740. Parvo_coat. 1 hit.
    PF08398. Parvo_coat_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF88645. SSF88645. 1 hit.

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform VP1 (identifier: P03136-1) [UniParc]FASTAAdd to Basket

    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

    MAPPAKRAKR GWVPPGYKYL GPGNSLDQGE PTNPSDAAAK EHDEAYDQYI    50
    KSGKNPYLYF SPADQRFIDQ TKDAKDWGGK VGHYFFRTKR AFAPKLSTDS 100
    EPGTSGVSRP GKRTKPPAHI FVNQARAKKK RASLAAQQRT LTMSDGTETN 150
    QPDTGIANAR VERSADGGGS SGGGGSGGGG IGVSTGTYDN QTTYKFLGDG 200
    WVEITAHASR LLHLGMPPSE NYCRVTVHNN QTTGHGTKVK GNMAYDTHQQ 250
    IWTPWSLVDA NAWGVWFQPS DWQFIQNSME SLNLDSLSQE LFNVVVKTVT 300
    EQQGAGQDAI KVYNNDLTAC MMVALDSNNI LPYTPAAQTS ETLGFYPWKP 350
    TAPAPYRYYF FMPRQLSVTS SNSAEGTQIT DTIGEPQALN SQFFTIENTL 400
    PITLLRTGDE FTTGTYIFNT DPLKLTHTWQ TNRHLACLQG ITDLPTSDTA 450
    TASLTANGDR FGSTQTQNVN YVTEALRTRP AQIGFMQPHD NFEANRGGPF 500
    KVPVVPLDIT AGEDHDANGA IRFNYGKQHG EDWAKQGAAP ERYTWDAIDS 550
    AAGRDTARCF VQSAPISIPP NQNQILQRED AIAGRTNMHY TNVFNSYGPL 600
    SAFPHPDPIY PNGQIWDKEL DLEHKPRLHV TAPFVCKNNP PGQLFVHLGP 650
    NLTDQFDPNS TTVSRIVTYS TFYWKGILKF KAKLRPNLTW NPVYQATTDS 700
    VANSYMNVKK WLPSATGNMH SDPLICRPVP HMTY 734

    Note: Minor splicing isoform.

    Length:734
    Mass (Da):81,053
    Last modified:April 5, 2011 - v2
    Checksum:i0AA6B088729203F8
    GO
    Isoform VP2 (identifier: P03136-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-142: Missing.

    Note: Major splicing isoform produced by deletion of the initiating AUG for VP1 and downstream translation of VP2.

    Show »
    Length:592
    Mass (Da):65,335
    Checksum:i924A603F290346CB
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 142142Missing in isoform VP2. CuratedVSP_041140Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X01457 Genomic DNA. Translation: CAB57285.1. Sequence problems.
    PIRiA03699. VCPVV2.
    RefSeqiNP_040319.1. NC_001358.1.

    Genome annotation databases

    GeneIDi1489602.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X01457 Genomic DNA. Translation: CAB57285.1 . Sequence problems.
    PIRi A03699. VCPVV2.
    RefSeqi NP_040319.1. NC_001358.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4G0R X-ray 2.70 A 1-734 [» ]
    4GBT X-ray 3.20 A 1-734 [» ]
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 1489602.

    Family and domain databases

    Gene3Di 2.170.30.10. 1 hit.
    InterProi IPR016184. Capsid/spike_ssDNA_virus.
    IPR001403. Parvovirus_coat.
    IPR013607. Parvovirus_coat_VP1_N.
    [Graphical view ]
    Pfami PF00740. Parvo_coat. 1 hit.
    PF08398. Parvo_coat_N. 1 hit.
    [Graphical view ]
    SUPFAMi SSF88645. SSF88645. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Parvovirus genome: nucleotide sequence of H-1 and mapping of its genes by hybrid-arrested translation."
      Rhode S.L. III, Paradiso P.R.
      J. Virol. 45:173-184(1983) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

    Entry informationi

    Entry nameiCAPSD_PAVHH
    AccessioniPrimary (citable) accession number: P03136
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: April 5, 2011
    Last modified: October 1, 2014
    This is version 74 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

    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