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P18546 (CAPSD_PAVPN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 78. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Capsid protein VP1
Alternative name(s):
Coat protein VP1
OrganismPorcine parvovirus (strain NADL-2) (PPV) [Complete proteome]
Taxonomic identifier10797 [NCBI]
Taxonomic lineageViruses › ssDNA viruses › Parvoviridae › Parvovirinae › Parvovirus ›
Virus hostSus scrofa (Pig) [TaxID: 9823]

Protein attributes

Sequence length729 AA.
Sequence statusComplete.
Protein existenceEvidence 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 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.

Subcellular location

Virion By similarity. Host nucleus 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

VP3 might be a post-translational cleavage product of VP2 in several autonomous parvoviruses.

Sequence similarities

Belongs to the parvoviridae capsid protein family.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform VP1 (identifier: P18546-1)

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: Minor splicing isoform.
Isoform VP2 (identifier: P18546-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-150: Missing.
Note: Major splicing isoform produced by deletion of the initiating AUG for VP1 and downstream translation of VP2.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 729729Capsid protein VP1
PRO_0000039437

Regions

Region18 – 6346Phospholipase A2-like By similarity
Motif4 – 129Nuclear localization signal Potential
Compositional bias175 – 19016Gly-rich

Sites

Metal binding3301Magnesium 1 By similarity

Natural variations

Alternative sequence1 – 150150Missing in isoform VP2.
VSP_041144

Experimental info

Sequence conflict101G → GKGSFKGVVAYILQIIFLYI TG in BAA00502. Ref.3
Sequence conflict16 – 183YKY → TI in BAA00502. Ref.3
Sequence conflict561Y → T in BAA00502. Ref.3
Sequence conflict1951T → S in BAA00502. Ref.3
Sequence conflict2421V → S in BAA00502. Ref.3
Sequence conflict2941E → A in BAA00502. Ref.3
Sequence conflict7051N → K in BAA00502. Ref.3
Sequence conflict7151R → K in BAA00502. Ref.3

Secondary structure

1 ....................................................................... 729
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform VP1 [UniParc].

Last modified November 1, 1990. Version 1.
Checksum: EF816E246C80DB42

FASTA72980,946
        10         20         30         40         50         60 
MAPPAKRARG LTLPGYKYLG PGNSLDQGEP TNPSDAAAKE HDEAYDKYIK SGKNPYFYFS 

        70         80         90        100        110        120 
AADEKFIKET EHAKDYGGKI GHYFFRAKRA FAPKLSETDS PTTSQQPEVR RSPRKHPGSK 

       130        140        150        160        170        180 
PPGKRPAPRH IFINLAKKKA KGTSNTNSNS MSENVEQHNP INAGTELSAT GNESGGGGGG 

       190        200        210        220        230        240 
GGGRGAGGVG VSTGTFNNQT EFQYLGEGLV RITAHASRLI HLNMPEHETY KRIHVLNSES 

       250        260        270        280        290        300 
GVAGQMVQDD AHTQMVTPWS LIDANAWGVW FNPADWQLIS NNMTEINLVS FEQEIFNVVL 

       310        320        330        340        350        360 
KTITESATSP PTKIYNNDLT ASLMVALDTN NTLPYTPAAP RSETLGFYPW LPTKPTQYRY 

       370        380        390        400        410        420 
YLSCIRNLNP PTYTGQSQQI TDSIQTGLHS DIMFYTIENA VPIHLLRTGD EFSTGIYHFD 

       430        440        450        460        470        480 
TKPLKLTHSW QTNRSLGLPP KLLTEPTTEG DQHPGTLPAA NTRKGYHQTI NNSYTEATAI 

       490        500        510        520        530        540 
RPAQVGYNTP YMNFEYSNGG PFLTPIVPTA DTQYNDDEPN GAIRFTMDYQ HGHLTTSSQE 

       550        560        570        580        590        600 
LERYTFNPQS KCGRAPKQQF NQQAPLNLEN TNNGTLLPSD PIGGKSNMHF MNTLNTYGPL 

       610        620        630        640        650        660 
TALNNTAPVF PNGQIWDKEL DTDLKPRLHV TAPFVCKNNP PGQLFVKIAP NLTDDFNADS 

       670        680        690        700        710        720 
PQQPRIITYS NFWWKGTLTF TAKMRSSNMW NPIQQHTTTA ENIGNYIPTN IGGIRMFPEY 


SQLIPRKLY

« Hide

Isoform VP2 [UniParc].

Checksum: E717F6CDA927F4B2
Show »

FASTA57964,358

References

[1]"Nucleotide sequence analysis of the capsid genes and the right-hand terminal palindrome of porcine parvovirus, strain NADL-2."
Vasudevacharya J., Basak S., Srinivas R.V., Compans R.W.
Virology 173:368-377(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The complete nucleotide sequence of an infectious clone of porcine parvovirus, strain NADL-2."
Vasudevacharya J., Basak S., Srinivas R.V., Compans R.W.
Virology 178:611-616(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"Porcine parvovirus: DNA sequence and genome organization."
Ranz A.I., Manclus J.J., Diaz-Aroca E., Casal J.I.
J. Gen. Virol. 70:2541-2553(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]"Genomic organization and mapping of transcription and translation products of the NADL-2 strain of porcine parvovirus."
Bergeron J., Menezes J., Tijssen P.
Virology 197:86-98(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE.
[5]"The structure of porcine parvovirus: comparison with related viruses."
Simpson A.A., Hebert B., Sullivan G.M., Parrish C.R., Zadori Z., Tijssen P., Rossmann M.G.
J. Mol. Biol. 315:1189-1198(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF 151-729.
+Additional computationally mapped references.

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		M32787 Genomic DNA. Translation: AAA46917.1.
M32787 Genomic DNA. Translation: AAA46918.1.
M38367 Genomic DNA. Translation: AAA46919.1.
M38367 Genomic DNA. Translation: AAA46921.1.
D00623 Genomic DNA. Translation: BAA00502.1.
L23427 Unassigned DNA. No translation available.
PIRVCPVPP. B33302.
VCPVNA. B33743.
RefSeqNP_757371.1. NC_001718.1.
NP_757372.1. NC_001718.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1K3VX-ray3.50A151-729[»]
ProteinModelPortalP18546.
SMRP18546. Positions 188-729.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID1489595.

Family and domain databases

Gene3D2.170.30.10. 1 hit.
InterProIPR016184. Capsid/spike_ssDNA_virus.
IPR001403. Parvovirus_coat.
IPR013607. Parvovirus_coat_VP1_N.
[Graphical view]
PfamPF00740. Parvo_coat. 1 hit.
PF08398. Parvo_coat_N. 1 hit.
[Graphical view]
SUPFAMSSF88645. Capsid/spike_ssDNA_virus. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP18546.

Entry information

Entry nameCAPSD_PAVPN
AccessionPrimary (citable) accession number: P18546
Secondary accession number(s): P22964, Q89816
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: November 1, 1990
Last modified: April 3, 2013
This is version 78 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·Documents