P03135 (CAPSD_AAV2S) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Capsid protein VP1 Alternative name(s): Coat protein VP1
Organism	Adeno-associated virus 2 (isolate Srivastava/1982) (AAV-2)
Taxonomic identifier	648242 [NCBI]
Taxonomic lineage	Viruses › ssDNA viruses › Parvoviridae › Parvovirinae › Dependovirus
Virus host	Mammalia [TaxID: 40674]

Protein attributes

Sequence length	735 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 size variants of the capsid proteins, which differ in the N-terminus. 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. Ref.4 Ref.5
Subcellular location	Virion Potential.
Domain	The N-terminus of VP1 is sequestered within the mature capsid. It contains a phospholipase A2-like region and putative nuclear localization signals.
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.
Sequence similarities	Belongs to the parvoviridae capsid protein family.
Sequence caution	The sequence AAA42376.1 differs from that shown. Reason: Frameshift at position 676.

Ontologies

Keywords
Biological process	Clathrin-mediated endocytosis of virus by host Host-virus interaction Initiation of viral infection Viral attachment to host cell Viral penetration into host cytoplasm Viral penetration via permeabilization of host organellar membrane Virus endocytosis by host
Cellular component	Virion
Coding sequence diversity	Alternative initiation Alternative splicing
Molecular function	Capsid protein T=1 icosahedral capsid protein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	interspecies interaction between organisms Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	structural molecule activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing and alternative initiation. [Align] [Select]

Isoform VP1 (identifier: P03135-1)

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.

Note: Produced by alternative splicing (2.6 kb mRNA).

Isoform VP2 (identifier: P03135-2)

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.

Isoform VP3 (identifier: P03135-3)

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.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 735

735

Capsid protein VP1

PRO_0000222455

Regions

Region

52 – 97

46

Phospholipase A2-like By similarity

Natural variations

Alternative sequence

1 – 202

202

Missing in isoform VP3.

VSP_040828

Alternative sequence

1 – 137

137

Missing in isoform VP2.

VSP_040829

Alternative sequence

138

1

T → M in isoform VP2.

VSP_040830

Experimental info

Sequence conflict

520 – 521

2

Missing in AAA42376. Ref.3

Sequence conflict

553

1

D → N in AAA42376. Ref.3

Sequence conflict

566

1

R → G in AAA42376. Ref.3

Secondary structure

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735

Helix Strand Turn

Details...

Beta strand

239 – 241

3

Beta strand

247 – 249

3

Helix

252 – 255

4

Helix

268 – 270

3

Helix

287 – 289

3

Helix

293 – 301

9

Beta strand

307 – 322

16

Beta strand

340 – 344

5

Beta strand

401 – 403

3

Beta strand

409 – 414

6

Beta strand

424 – 428

5

Beta strand

430 – 432

3

Beta strand

441 – 451

11

Beta strand

456 – 464

9

Helix

470 – 472

3

Beta strand

487 – 491

5

Turn

492 – 494

3

Beta strand

507 – 509

3

Beta strand

514 – 516

3

Beta strand

531 – 533

3

Beta strand

547 – 549

3

Helix

552 – 554

3

Helix

561 – 563

3

Turn

564 – 566

3

Beta strand

594 – 596

3

Beta strand

644 – 648

5

Beta strand

671 – 673

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform VP1 [UniParc]. Last modified April 5, 2011. Version 2. Checksum: 980BEEF46908390B	FASTA	735	81,945
	10 20 30 40 50 60 MAADGYLPDW LEDTLSEGIR QWWKLKPGPP PPKPAERHKD DSRGLVLPGY KYLGPFNGLD 70 80 90 100 110 120 KGEPVNEADA AALEHDKAYD RQLDSGDNPY LKYNHADAEF QERLKEDTSF GGNLGRAVFQ 130 140 150 160 170 180 AKKRVLEPLG LVEEPVKTAP GKKRPVEHSP VEPDSSSGTG KAGQQPARKR LNFGQTGDAD 190 200 210 220 230 240 SVPDPQPLGQ PPAAPSGLGT NTMATGSGAP MADNNEGADG VGNSSGNWHC DSTWMGDRVI 250 260 270 280 290 300 TTSTRTWALP TYNNHLYKQI SSQSGASNDN HYFGYSTPWG YFDFNRFHCH FSPRDWQRLI 310 320 330 340 350 360 NNNWGFRPKR LNFKLFNIQV KEVTQNDGTT TIANNLTSTV QVFTDSEYQL PYVLGSAHQG 370 380 390 400 410 420 CLPPFPADVF MVPQYGYLTL NNGSQAVGRS SFYCLEYFPS QMLRTGNNFT FSYTFEDVPF 430 440 450 460 470 480 HSSYAHSQSL DRLMNPLIDQ YLYYLSRTNT PSGTTTQSRL QFSQAGASDI RDQSRNWLPG 490 500 510 520 530 540 PCYRQQRVSK TSADNNNSEY SWTGATKYHL NGRDSLVNPG PAMASHKDDE EKFFPQSGVL 550 560 570 580 590 600 IFGKQGSEKT NVDIEKVMIT DEEEIRTTNP VATEQYGSVS TNLQRGNRQA ATADVNTQGV 610 620 630 640 650 660 LPGMVWQDRD VYLQGPIWAK IPHTDGHFHP SPLMGGFGLK HPPPQILIKN TPVPANPSTT 670 680 690 700 710 720 FSAAKFASFI TQYSTGQVSV EIEWELQKEN SKRWNPEIQY TSNYNKSVNV DFTVDTNGVY 730 SEPRPIGTRY LTRNL
	Isoform VP2 [UniParc]. Checksum: 070811ED9368E934	FASTA	598	66,620
	10 20 30 40 50 60 MAPGKKRPVE HSPVEPDSSS GTGKAGQQPA RKRLNFGQTG DADSVPDPQP LGQPPAAPSG 70 80 90 100 110 120 LGTNTMATGS GAPMADNNEG ADGVGNSSGN WHCDSTWMGD RVITTSTRTW ALPTYNNHLY 130 140 150 160 170 180 KQISSQSGAS NDNHYFGYST PWGYFDFNRF HCHFSPRDWQ RLINNNWGFR PKRLNFKLFN 190 200 210 220 230 240 IQVKEVTQND GTTTIANNLT STVQVFTDSE YQLPYVLGSA HQGCLPPFPA DVFMVPQYGY 250 260 270 280 290 300 LTLNNGSQAV GRSSFYCLEY FPSQMLRTGN NFTFSYTFED VPFHSSYAHS QSLDRLMNPL 310 320 330 340 350 360 IDQYLYYLSR TNTPSGTTTQ SRLQFSQAGA SDIRDQSRNW LPGPCYRQQR VSKTSADNNN 370 380 390 400 410 420 SEYSWTGATK YHLNGRDSLV NPGPAMASHK DDEEKFFPQS GVLIFGKQGS EKTNVDIEKV 430 440 450 460 470 480 MITDEEEIRT TNPVATEQYG SVSTNLQRGN RQAATADVNT QGVLPGMVWQ DRDVYLQGPI 490 500 510 520 530 540 WAKIPHTDGH FHPSPLMGGF GLKHPPPQIL IKNTPVPANP STTFSAAKFA SFITQYSTGQ 550 560 570 580 590 VSVEIEWELQ KENSKRWNPE IQYTSNYNKS VNVDFTVDTN GVYSEPRPIG TRYLTRNL
	Isoform VP3 [UniParc]. Checksum: 9E4D8BC25810D4F0	FASTA	533	60,063
	10 20 30 40 50 60 MATGSGAPMA DNNEGADGVG NSSGNWHCDS TWMGDRVITT STRTWALPTY NNHLYKQISS 70 80 90 100 110 120 QSGASNDNHY FGYSTPWGYF DFNRFHCHFS PRDWQRLINN NWGFRPKRLN FKLFNIQVKE 130 140 150 160 170 180 VTQNDGTTTI ANNLTSTVQV FTDSEYQLPY VLGSAHQGCL PPFPADVFMV PQYGYLTLNN 190 200 210 220 230 240 GSQAVGRSSF YCLEYFPSQM LRTGNNFTFS YTFEDVPFHS SYAHSQSLDR LMNPLIDQYL 250 260 270 280 290 300 YYLSRTNTPS GTTTQSRLQF SQAGASDIRD QSRNWLPGPC YRQQRVSKTS ADNNNSEYSW 310 320 330 340 350 360 TGATKYHLNG RDSLVNPGPA MASHKDDEEK FFPQSGVLIF GKQGSEKTNV DIEKVMITDE 370 380 390 400 410 420 EEIRTTNPVA TEQYGSVSTN LQRGNRQAAT ADVNTQGVLP GMVWQDRDVY LQGPIWAKIP 430 440 450 460 470 480 HTDGHFHPSP LMGGFGLKHP PPQILIKNTP VPANPSTTFS AAKFASFITQ YSTGQVSVEI 490 500 510 520 530 EWELQKENSK RWNPEIQYTS NYNKSVNVDF TVDTNGVYSE PRPIGTRYLT RNL

References

[1]	"Nucleotide sequence and organization of the adeno-associated virus 2 genome." Srivastava A., Lusby E.W., Berns K.I. J. Virol. 45:555-564(1983) [PubMed: 6300419] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Mutations in the carboxy terminus of adeno-associated virus 2 capsid proteins affect viral infectivity: lack of an RGD integrin-binding motif." Ruffing M., Heid H., Kleinschmidt J.A. J. Gen. Virol. 75:3385-3392(1994) [PubMed: 7996133] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	Berns K.I., Bohenzky R.A., Cassinotti P., Colvin D., Donahue B.A., Dull T., Horer M., Kleinschmidt J.A., Ruffing M., Snyder R.O., Tratschin J.-D., Weitz M. Submitted (JAN-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Infectious entry pathway of adeno-associated virus and adeno-associated virus vectors." Bartlett J.S., Wilcher R., Samulski R.J. J. Virol. 74:2777-2785(2000) [PubMed: 10684294] [Abstract] Cited for: FUNCTION.
[5]	"The VP1 capsid protein of adeno-associated virus type 2 is carrying a phospholipase A2 domain required for virus infectivity." Girod A., Wobus C.E., Zadori Z., Ried M., Leike K., Tijssen P., Kleinschmidt J.A., Hallek M. J. Gen. Virol. 83:973-978(2002) [PubMed: 11961250] [Abstract] Cited for: FUNCTION OF VP1.
[6]	"The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy." Xie Q., Bu W., Bhatia S., Hare J., Somasundaram T., Azzi A., Chapman M.S. Proc. Natl. Acad. Sci. U.S.A. 99:10405-10410(2002) [PubMed: 12136130] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 217-735.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

VCPV3A. A03698.

RefSeq

YP_680426.1. NC_001401.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1LP3	X-ray	3.00	A	217-735	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-46114N.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

4192017.

Family and domain databases

InterPro

IPR016184. Capsid/spike_ssDNA_virus.
IPR001403. Parvovirus_coat.
IPR013607. Parvovirus_coat_VP1_N.
[Graphical view]

Gene3D

G3DSA:2.170.30.10. Parvo_coat. 1 hit.

Pfam

PF00740. Parvo_coat. 1 hit.
PF08398. Parvo_coat_N. 1 hit.
[Graphical view]

SUPFAM

SSF88645. Capsid/spike_ssDNA_virus. 1 hit.

ProtoNet

Search...

Entry information

Entry name

CAPSD_AAV2S

Accession

Primary (citable) accession number: P03135
Secondary accession number(s): O56652, O56653, O92917

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	April 5, 2011
Last modified:	January 25, 2012
This is version 59 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program