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P03136

- CAPSD_PAVHH

UniProt

P03136 - CAPSD_PAVHH

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Protein

Capsid protein VP1

Gene
N/A
Organism
Hamster parvovirus H1
Status
Reviewed - Annotation score: 3 out of 5 - Experimental evidence at protein leveli

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi328 – 3281Magnesium 1 By 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
Complete GO annotation...

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 Reviewed prediction

GO - Cellular componenti

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

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[»]

Family & Domainsi

Region

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

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi4 – 1310Nuclear localization signal Reviewed prediction

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

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. VSP_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: September 3, 2014
This is version 73 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

Similar proteinsi