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Protein

Capsid protein VP1

Gene
N/A
Organism
Hamster parvovirus H1
Status
Reviewed-Annotation score: 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).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi328Magnesium 1By similarity1

GO - Molecular functioni

GO - Biological processi

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]
Proteomesi
  • UP000007897 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000394311 – 734Capsid protein VP1Add BLAST734

Structurei

Secondary structure

1734
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi192 – 198Combined sources7
Beta strandi201 – 215Combined sources15
Beta strandi218 – 221Combined sources4
Beta strandi223 – 227Combined sources5
Beta strandi232 – 235Combined sources4
Beta strandi237 – 239Combined sources3
Helixi243 – 245Combined sources3
Beta strandi248 – 257Combined sources10
Helixi263 – 266Combined sources4
Helixi269 – 278Combined sources10
Beta strandi279 – 301Combined sources23
Beta strandi311 – 315Combined sources5
Beta strandi321 – 325Combined sources5
Helixi336 – 339Combined sources4
Beta strandi354 – 360Combined sources7
Beta strandi364 – 366Combined sources3
Beta strandi381 – 383Combined sources3
Helixi388 – 390Combined sources3
Helixi396 – 399Combined sources4
Beta strandi403 – 405Combined sources3
Beta strandi426 – 428Combined sources3
Helixi432 – 434Combined sources3
Beta strandi441 – 443Combined sources3
Turni457 – 459Combined sources3
Turni474 – 476Combined sources3
Beta strandi480 – 484Combined sources5
Beta strandi492 – 495Combined sources4
Beta strandi498 – 501Combined sources4
Turni510 – 513Combined sources4
Helixi516 – 518Combined sources3
Beta strandi521 – 525Combined sources5
Helixi527 – 529Combined sources3
Beta strandi541 – 545Combined sources5
Beta strandi550 – 552Combined sources3
Helixi556 – 558Combined sources3
Beta strandi560 – 562Combined sources3
Helixi572 – 574Combined sources3
Beta strandi575 – 580Combined sources6
Helixi590 – 592Combined sources3
Turni610 – 612Combined sources3
Beta strandi622 – 624Combined sources3
Beta strandi633 – 635Combined sources3
Beta strandi644 – 648Combined sources5
Beta strandi668 – 684Combined sources17
Helixi708 – 711Combined sources4
Beta strandi729 – 731Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4G0RX-ray2.70A1-734[»]
4GBTX-ray3.20A1-734[»]
SMRiP03136.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni19 – 64Phospholipase A2-likeBy similarityAdd BLAST46

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi4 – 13Nuclear localization signalSequence analysis10

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi166 – 182Gly-richAdd BLAST17

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. AlignAdd to basket

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

        10         20         30         40         50
MAPPAKRAKR GWVPPGYKYL GPGNSLDQGE PTNPSDAAAK EHDEAYDQYI
60 70 80 90 100
KSGKNPYLYF SPADQRFIDQ TKDAKDWGGK VGHYFFRTKR AFAPKLSTDS
110 120 130 140 150
EPGTSGVSRP GKRTKPPAHI FVNQARAKKK RASLAAQQRT LTMSDGTETN
160 170 180 190 200
QPDTGIANAR VERSADGGGS SGGGGSGGGG IGVSTGTYDN QTTYKFLGDG
210 220 230 240 250
WVEITAHASR LLHLGMPPSE NYCRVTVHNN QTTGHGTKVK GNMAYDTHQQ
260 270 280 290 300
IWTPWSLVDA NAWGVWFQPS DWQFIQNSME SLNLDSLSQE LFNVVVKTVT
310 320 330 340 350
EQQGAGQDAI KVYNNDLTAC MMVALDSNNI LPYTPAAQTS ETLGFYPWKP
360 370 380 390 400
TAPAPYRYYF FMPRQLSVTS SNSAEGTQIT DTIGEPQALN SQFFTIENTL
410 420 430 440 450
PITLLRTGDE FTTGTYIFNT DPLKLTHTWQ TNRHLACLQG ITDLPTSDTA
460 470 480 490 500
TASLTANGDR FGSTQTQNVN YVTEALRTRP AQIGFMQPHD NFEANRGGPF
510 520 530 540 550
KVPVVPLDIT AGEDHDANGA IRFNYGKQHG EDWAKQGAAP ERYTWDAIDS
560 570 580 590 600
AAGRDTARCF VQSAPISIPP NQNQILQRED AIAGRTNMHY TNVFNSYGPL
610 620 630 640 650
SAFPHPDPIY PNGQIWDKEL DLEHKPRLHV TAPFVCKNNP PGQLFVHLGP
660 670 680 690 700
NLTDQFDPNS TTVSRIVTYS TFYWKGILKF KAKLRPNLTW NPVYQATTDS
710 720 730
VANSYMNVKK WLPSATGNMH SDPLICRPVP HMTY
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)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0411401 – 142Missing in isoform VP2. CuratedAdd BLAST142

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01457 Genomic DNA. Translation: CAB57285.1. Sequence problems.
PIRiA03699. VCPVV2.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X01457 Genomic DNA. Translation: CAB57285.1. Sequence problems.
PIRiA03699. VCPVV2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4G0RX-ray2.70A1-734[»]
4GBTX-ray3.20A1-734[»]
SMRiP03136.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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.
ProtoNetiSearch...

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: November 30, 2016
This is version 86 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.