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Protein

Capsid protein VP1

Gene

VP1

Organism
Adeno-associated virus 2 (isolate Srivastava/1982) (AAV-2)
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 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

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 nucleushost 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.

Structurei

Secondary structure

1735
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi221 – 223Combined sources3
Beta strandi232 – 234Combined sources3
Beta strandi239 – 241Combined sources3
Beta strandi244 – 249Combined sources6
Helixi252 – 255Combined sources4
Beta strandi258 – 261Combined sources4
Helixi268 – 270Combined sources3
Beta strandi273 – 282Combined sources10
Helixi287 – 289Combined sources3
Helixi293 – 301Combined sources9
Beta strandi302 – 322Combined sources21
Beta strandi340 – 344Combined sources5
Beta strandi374 – 378Combined sources5
Beta strandi401 – 403Combined sources3
Beta strandi409 – 414Combined sources6
Beta strandi424 – 428Combined sources5
Beta strandi430 – 432Combined sources3
Beta strandi441 – 452Combined sources12
Beta strandi455 – 464Combined sources10
Turni467 – 469Combined sources3
Helixi470 – 472Combined sources3
Beta strandi487 – 491Combined sources5
Turni492 – 494Combined sources3
Turni501 – 504Combined sources4
Beta strandi507 – 510Combined sources4
Beta strandi513 – 516Combined sources4
Beta strandi533 – 539Combined sources7
Beta strandi541 – 543Combined sources3
Beta strandi549 – 551Combined sources3
Helixi554 – 556Combined sources3
Beta strandi557 – 559Combined sources3
Helixi563 – 565Combined sources3
Turni566 – 568Combined sources3
Beta strandi576 – 579Combined sources4
Beta strandi593 – 598Combined sources6
Beta strandi618 – 620Combined sources3
Beta strandi635 – 641Combined sources7
Beta strandi646 – 650Combined sources5
Beta strandi673 – 688Combined sources16
Beta strandi711 – 714Combined sources4
Beta strandi731 – 733Combined sources3

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[»]
ProteinModelPortaliP03135.
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.
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:4192016.
vg:4192017.

Keywords - Coding sequence diversityi

Alternative initiation, Alternative splicing

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[»]
ProteinModelPortaliP03135.
SMRiP03135.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-46114N.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi4192015.
4192016.
4192017.
KEGGivg: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.
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: March 15, 2017
This is version 86 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

3D-structure, Complete proteome, Reference 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.