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Protein

Capsid protein VP1

Gene

VP1

Organism
Adeno-associated virus 2 (isolate Srivastava/1982) (AAV-2)
Status
Reviewed-Annotation score: -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 three size variants of the capsid protein VP1, VP2 and VP3 which differ in their N-terminus. The capsid encapsulates the genomic ssDNA. Binds to host cell heparan sulfate and uses host ITGA5-ITGB1 as coreceptor on the cell surface to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-dependent endocytosis. Binding to the host receptor 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.4 Publications

Miscellaneous

the ratio at which VP1, VP2 and VP3 proteins are synthesized in vivo is about 1:1:20, which is the same as in the mature virus particle.

GO - Molecular functioni

GO - Biological processi

Keywordsi

Biological processClathrin-mediated endocytosis of virus by host, Host-virus interaction, Viral attachment to host cell, Viral penetration into host cytoplasm, Viral penetration via permeabilization of host membrane, Virus endocytosis by host, Virus entry into host cell

Enzyme and pathway databases

BRENDAi3.1.1.4 11447

Names & Taxonomyi

Protein namesi
Recommended name:
Capsid protein VP1
Gene namesi
Name:VP1
OrganismiAdeno-associated virus 2 (isolate Srivastava/1982) (AAV-2)
Taxonomic identifieri648242 [NCBI]
Taxonomic lineageiVirusesssDNA virusesParvoviridaeParvovirinaeDependoparvovirus
Virus hostiMammalia [TaxID: 40674]
Proteomesi
  • UP000008469 Componenti: Genome
  • UP000180764 Componenti: Genome

Subcellular locationi

  • Virion Curated
  • host nucleolus 1 Publication
  • Note: Capid proteins are first observed in the host nucleolus where capsid assembly may occur, and then are present over the whole nucleoplasm where encapsidation of the viral DNA takes place.

GO - Cellular componenti

Keywords - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002224551 – 735Capsid protein VP1Add BLAST735

Interactioni

Protein-protein interaction databases

DIPiDIP-46114N
ELMiP03135

Structurei

Secondary structure

1735
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SMRiP03135
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03135

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni52 – 97Phospholipase A2-likeBy similarityAdd BLAST46

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

Phylogenomic databases

KOiK19252
OrthoDBiVOG0900002T

Family and domain databases

Gene3Di2.170.30.10, 1 hit
InterProiView protein in InterPro
IPR016184 Capsid/spike_ssDNA_virus
IPR001403 Parvovirus_coat
IPR013607 Parvovirus_coat_VP1_N
IPR036952 VP1/VP2
PfamiView protein in Pfam
PF00740 Parvo_coat, 1 hit
PF08398 Parvo_coat_N, 1 hit
SUPFAMiSSF88645 SSF88645, 1 hit

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing and alternative initiation. AlignAdd to basket
Isoform VP1 (identifier: P03135-1) [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
MAADGYLPDW LEDTLSEGIR QWWKLKPGPP PPKPAERHKD DSRGLVLPGY
60 70 80 90 100
KYLGPFNGLD KGEPVNEADA AALEHDKAYD RQLDSGDNPY LKYNHADAEF
110 120 130 140 150
QERLKEDTSF GGNLGRAVFQ AKKRVLEPLG LVEEPVKTAP GKKRPVEHSP
160 170 180 190 200
VEPDSSSGTG KAGQQPARKR LNFGQTGDAD SVPDPQPLGQ PPAAPSGLGT
210 220 230 240 250
NTMATGSGAP MADNNEGADG VGNSSGNWHC DSTWMGDRVI TTSTRTWALP
260 270 280 290 300
TYNNHLYKQI SSQSGASNDN HYFGYSTPWG YFDFNRFHCH FSPRDWQRLI
310 320 330 340 350
NNNWGFRPKR LNFKLFNIQV KEVTQNDGTT TIANNLTSTV QVFTDSEYQL
360 370 380 390 400
PYVLGSAHQG CLPPFPADVF MVPQYGYLTL NNGSQAVGRS SFYCLEYFPS
410 420 430 440 450
QMLRTGNNFT FSYTFEDVPF HSSYAHSQSL DRLMNPLIDQ YLYYLSRTNT
460 470 480 490 500
PSGTTTQSRL QFSQAGASDI RDQSRNWLPG PCYRQQRVSK TSADNNNSEY
510 520 530 540 550
SWTGATKYHL NGRDSLVNPG PAMASHKDDE EKFFPQSGVL IFGKQGSEKT
560 570 580 590 600
NVDIEKVMIT DEEEIRTTNP VATEQYGSVS TNLQRGNRQA ATADVNTQGV
610 620 630 640 650
LPGMVWQDRD VYLQGPIWAK IPHTDGHFHP SPLMGGFGLK HPPPQILIKN
660 670 680 690 700
TPVPANPSTT FSAAKFASFI TQYSTGQVSV EIEWELQKEN SKRWNPEIQY
710 720 730
TSNYNKSVNV DFTVDTNGVY SEPRPIGTRY LTRNL
Note: Produced by alternative splicing (2.6 kb mRNA).
Length:735
Mass (Da):81,945
Last modified:April 5, 2011 - v2
Checksum:i980BEEF46908390B
GO
Isoform VP2 (identifier: P03135-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-137: Missing.
     138-138: T → M

Note: Produced by alternative splicing (2.3 kb mRNA), with initiatory methionine encoded by an ACG codon.
Show »
Length:598
Mass (Da):66,620
Checksum:i070811ED9368E934
GO
Isoform VP3 (identifier: P03135-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-202: Missing.

Note: Produced by alternative initiation of the 2.3 kb mRNA.
Show »
Length:533
Mass (Da):60,063
Checksum:i9E4D8BC25810D4F0
GO

Sequence cautioni

The sequence AAA42376 differs from that shown. Reason: Frameshift at position 676.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti520 – 521Missing in AAA42376 (Ref. 3) Curated2
Sequence conflicti553D → N in AAA42376 (Ref. 3) Curated1
Sequence conflicti566R → G in AAA42376 (Ref. 3) Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0408281 – 202Missing in isoform VP3. CuratedAdd BLAST202
Alternative sequenceiVSP_0408291 – 137Missing in isoform VP2. CuratedAdd BLAST137
Alternative sequenceiVSP_040830138T → M in isoform VP2. Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01901 Genomic DNA Translation: AAA42376.1 Frameshift.
AF043303 Genomic DNA Translation: AAC03779.1
AF043303 Genomic DNA Translation: AAC03780.1
AF043303 Genomic DNA Translation: AAC03778.1
PIRiA03698 VCPV3A
RefSeqiYP_680426.1, NC_001401.2
YP_680427.1, NC_001401.2
YP_680428.1, NC_001401.2

Genome annotation databases

GeneIDi4192015
4192016
4192017
KEGGivg:4192015
vg:4192016
vg:4192017

Keywords - Coding sequence diversityi

Alternative initiation, Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01901 Genomic DNA Translation: AAA42376.1 Frameshift.
AF043303 Genomic DNA Translation: AAC03779.1
AF043303 Genomic DNA Translation: AAC03780.1
AF043303 Genomic DNA Translation: AAC03778.1
PIRiA03698 VCPV3A
RefSeqiYP_680426.1, NC_001401.2
YP_680427.1, NC_001401.2
YP_680428.1, NC_001401.2

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LP3X-ray3.00A217-735[»]
3J1Selectron microscopy8.50A217-735[»]
3J4Pelectron microscopy4.80A221-735[»]
5IPIelectron microscopy3.801/2/3/4/5/6/7/8/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V1-735[»]
5IPKelectron microscopy3.701/2/3/4/5/6/7/8/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V1-735[»]
6CBEelectron microscopy2.780/1/2/3/4/5/6/7/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V1-735[»]
6E9Delectron microscopy1.861/2/3/4/5/6/7/8/A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V1-735[»]
SMRiP03135
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-46114N
ELMiP03135

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi4192015
4192016
4192017
KEGGivg:4192015
vg:4192016
vg:4192017

Phylogenomic databases

KOiK19252
OrthoDBiVOG0900002T

Enzyme and pathway databases

BRENDAi3.1.1.4 11447

Miscellaneous databases

EvolutionaryTraceiP03135

Family and domain databases

Gene3Di2.170.30.10, 1 hit
InterProiView protein in InterPro
IPR016184 Capsid/spike_ssDNA_virus
IPR001403 Parvovirus_coat
IPR013607 Parvovirus_coat_VP1_N
IPR036952 VP1/VP2
PfamiView protein in Pfam
PF00740 Parvo_coat, 1 hit
PF08398 Parvo_coat_N, 1 hit
SUPFAMiSSF88645 SSF88645, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiCAPSD_AAV2S
AccessioniPrimary (citable) accession number: P03135
Secondary accession number(s): O56652, O56653, O92917
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: April 5, 2011
Last modified: October 10, 2018
This is version 93 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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