CAPSD_PAVPN
ID CAPSD_PAVPN Reviewed; 729 AA.
AC P18546; P22964; Q89816;
DT 01-NOV-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1990, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=Capsid protein VP1;
DE AltName: Full=Coat protein VP1;
OS Porcine parvovirus (strain NADL-2) (PPV).
OC Viruses; Monodnaviria; Shotokuvirae; Cossaviricota; Quintoviricetes;
OC Piccovirales; Parvoviridae; Parvovirinae; Protoparvovirus.
OX NCBI_TaxID=10797;
OH NCBI_TaxID=9823; Sus scrofa (Pig).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2596019; DOI=10.1016/0042-6822(89)90549-7;
RA Vasudevacharya J., Basak S., Srinivas R.V., Compans R.W.;
RT "Nucleotide sequence analysis of the capsid genes and the right-hand
RT terminal palindrome of porcine parvovirus, strain NADL-2.";
RL Virology 173:368-377(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2219713; DOI=10.1016/0042-6822(90)90364-w;
RA Vasudevacharya J., Basak S., Srinivas R.V., Compans R.W.;
RT "The complete nucleotide sequence of an infectious clone of porcine
RT parvovirus, strain NADL-2.";
RL Virology 178:611-616(1990).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2794971; DOI=10.1099/0022-1317-70-10-2541;
RA Ranz A.I., Manclus J.J., Diaz-Aroca E., Casal J.I.;
RT "Porcine parvovirus: DNA sequence and genome organization.";
RL J. Gen. Virol. 70:2541-2553(1989).
RN [4]
RP NUCLEOTIDE SEQUENCE.
RX PubMed=8212598; DOI=10.1006/viro.1993.1569;
RA Bergeron J., Menezes J., Tijssen P.;
RT "Genomic organization and mapping of transcription and translation products
RT of the NADL-2 strain of porcine parvovirus.";
RL Virology 197:86-98(1993).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (3.5 ANGSTROMS) OF 151-729.
RX PubMed=11827486; DOI=10.1006/jmbi.2001.5319;
RA Simpson A.A., Hebert B., Sullivan G.M., Parrish C.R., Zadori Z.,
RA Tijssen P., Rossmann M.G.;
RT "The structure of porcine parvovirus: comparison with related viruses.";
RL J. Mol. Biol. 315:1189-1198(2002).
CC -!- FUNCTION: Capsid protein self-assembles to form an icosahedral capsid
CC with a T=1 symmetry, about 22 nm in diameter, and consisting of 60
CC copies of two size variants of the capsid proteins, VP1 and VP2, which
CC differ by the presence of an N-terminal extension in the minor protein
CC VP1. The capsid encapsulates the genomic ssDNA. Capsid proteins are
CC responsible for the attachment to host cell receptors. This attachment
CC induces virion internalization predominantly through clathrin-dependent
CC endocytosis. Binding to the host receptors also induces capsid
CC rearrangements leading to surface exposure of VP1 N-terminus,
CC specifically its phospholipase A2-like region and putative nuclear
CC localization signal(s). VP1 N-terminus might serve as a lipolytic
CC enzyme to breach the endosomal membrane during entry into host cell and
CC might contribute to virus transport to the nucleus (By similarity).
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Virion {ECO:0000250}. Host nucleus {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=VP1;
CC IsoId=P18546-1; Sequence=Displayed;
CC Name=VP2;
CC IsoId=P18546-2; Sequence=VSP_041144;
CC -!- DOMAIN: The N-terminus of VP1 is sequestered within the mature capsid.
CC It contains a phospholipase A2-like region and putative nuclear
CC localization signals.
CC -!- MISCELLANEOUS: VP3 might be a post-translational cleavage product of
CC VP2 in several autonomous parvoviruses.
CC -!- MISCELLANEOUS: [Isoform VP1]: Minor splicing isoform.
CC -!- MISCELLANEOUS: [Isoform VP2]: Major splicing isoform produced by
CC deletion of the initiating AUG for VP1 and downstream translation of
CC VP2. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the parvoviridae capsid protein family.
CC {ECO:0000305}.
CC -!- WEB RESOURCE: Name=Virus Particle ExploreR db; Note=Icosahedral capsid
CC structure;
CC URL="https://viperdb.scripps.edu/Info_Page.php?VDB=1k3v";
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DR EMBL; M32787; AAA46917.1; -; Genomic_DNA.
DR EMBL; M32787; AAA46918.1; -; Genomic_DNA.
DR EMBL; M38367; AAA46919.1; -; Genomic_DNA.
DR EMBL; M38367; AAA46921.1; -; Genomic_DNA.
DR EMBL; D00623; BAA00502.1; -; Genomic_DNA.
DR EMBL; L23427; -; NOT_ANNOTATED_CDS; Unassigned_DNA.
DR PIR; B33302; VCPVPP.
DR PIR; B33743; VCPVNA.
DR RefSeq; NP_757371.1; NC_001718.1.
DR RefSeq; NP_757372.1; NC_001718.1.
DR PDB; 1K3V; X-ray; 3.50 A; A=151-729.
DR PDBsum; 1K3V; -.
DR SMR; P18546; -.
DR GeneID; 1489595; -.
DR KEGG; vg:1489595; -.
DR EvolutionaryTrace; P18546; -.
DR Proteomes; UP000008155; Genome.
DR GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0039615; C:T=1 icosahedral viral capsid; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR GO; GO:0075512; P:clathrin-dependent endocytosis of virus by host cell; IEA:UniProtKB-KW.
DR GO; GO:0075521; P:microtubule-dependent intracellular transport of viral material towards nucleus; IEA:UniProtKB-KW.
DR GO; GO:0039665; P:permeabilization of host organelle membrane involved in viral entry into host cell; IEA:UniProtKB-KW.
DR GO; GO:0099008; P:viral entry via permeabilization of inner membrane; IEA:UniProtKB-KW.
DR GO; GO:0075732; P:viral penetration into host nucleus; IEA:UniProtKB-KW.
DR GO; GO:0019062; P:virion attachment to host cell; IEA:UniProtKB-KW.
DR Gene3D; 2.170.30.10; -; 1.
DR InterPro; IPR016184; Capsid/spike_ssDNA_virus.
DR InterPro; IPR001403; Parvovirus_coat.
DR InterPro; IPR013607; Phospholipase_A2-like.
DR InterPro; IPR036952; VP1/VP2.
DR Pfam; PF00740; Parvo_coat; 1.
DR Pfam; PF08398; Phospholip_A2_4; 1.
DR SUPFAM; SSF88645; SSF88645; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Capsid protein;
KW Clathrin-mediated endocytosis of virus by host;
KW Cytoplasmic inwards viral transport; Host nucleus; Host-virus interaction;
KW Magnesium; Metal-binding; Microtubular inwards viral transport;
KW T=1 icosahedral capsid protein; Viral attachment to host cell;
KW Viral penetration into host cytoplasm; Viral penetration into host nucleus;
KW Viral penetration via permeabilization of host membrane; Virion;
KW Virus endocytosis by host; Virus entry into host cell.
FT CHAIN 1..729
FT /note="Capsid protein VP1"
FT /id="PRO_0000039437"
FT REGION 1..37
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 18..63
FT /note="Phospholipase A2-like"
FT /evidence="ECO:0000250"
FT REGION 94..129
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 163..186
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 437..465
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 4..12
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255"
FT BINDING 330
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1..150
FT /note="Missing (in isoform VP2)"
FT /evidence="ECO:0000305"
FT /id="VSP_041144"
FT CONFLICT 10
FT /note="G -> GKGSFKGVVAYILQIIFLYITG (in Ref. 3; BAA00502)"
FT /evidence="ECO:0000305"
FT CONFLICT 16..18
FT /note="YKY -> TI (in Ref. 3; BAA00502)"
FT /evidence="ECO:0000305"
FT CONFLICT 56
FT /note="Y -> T (in Ref. 3; BAA00502)"
FT /evidence="ECO:0000305"
FT CONFLICT 195
FT /note="T -> S (in Ref. 3; BAA00502)"
FT /evidence="ECO:0000305"
FT CONFLICT 242
FT /note="V -> S (in Ref. 3; BAA00502)"
FT /evidence="ECO:0000305"
FT CONFLICT 294
FT /note="E -> A (in Ref. 3; BAA00502)"
FT /evidence="ECO:0000305"
FT CONFLICT 705
FT /note="N -> K (in Ref. 3; BAA00502)"
FT /evidence="ECO:0000305"
FT CONFLICT 715
FT /note="R -> K (in Ref. 3; BAA00502)"
FT /evidence="ECO:0000305"
FT STRAND 200..205
FT /evidence="ECO:0007829|PDB:1K3V"
FT HELIX 206..208
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 209..223
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 231..235
FT /evidence="ECO:0007829|PDB:1K3V"
FT HELIX 238..241
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 242..244
FT /evidence="ECO:0007829|PDB:1K3V"
FT HELIX 245..248
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 252..261
FT /evidence="ECO:0007829|PDB:1K3V"
FT HELIX 267..270
FT /evidence="ECO:0007829|PDB:1K3V"
FT HELIX 273..282
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 283..292
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 294..306
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 308..310
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 312..317
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 323..328
FT /evidence="ECO:0007829|PDB:1K3V"
FT HELIX 339..341
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 356..361
FT /evidence="ECO:0007829|PDB:1K3V"
FT HELIX 389..391
FT /evidence="ECO:0007829|PDB:1K3V"
FT HELIX 397..400
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 403..406
FT /evidence="ECO:0007829|PDB:1K3V"
FT HELIX 433..435
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 447..450
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 468..472
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 482..486
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 494..497
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 500..503
FT /evidence="ECO:0007829|PDB:1K3V"
FT HELIX 518..520
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 531..533
FT /evidence="ECO:0007829|PDB:1K3V"
FT TURN 556..558
FT /evidence="ECO:0007829|PDB:1K3V"
FT HELIX 590..592
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 622..624
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 633..635
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 643..648
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 658..662
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 668..684
FT /evidence="ECO:0007829|PDB:1K3V"
FT STRAND 689..691
FT /evidence="ECO:0007829|PDB:1K3V"
FT TURN 700..702
FT /evidence="ECO:0007829|PDB:1K3V"
FT HELIX 703..706
FT /evidence="ECO:0007829|PDB:1K3V"
SQ SEQUENCE 729 AA; 80946 MW; EF816E246C80DB42 CRC64;
MAPPAKRARG LTLPGYKYLG PGNSLDQGEP TNPSDAAAKE HDEAYDKYIK SGKNPYFYFS
AADEKFIKET EHAKDYGGKI GHYFFRAKRA FAPKLSETDS PTTSQQPEVR RSPRKHPGSK
PPGKRPAPRH IFINLAKKKA KGTSNTNSNS MSENVEQHNP INAGTELSAT GNESGGGGGG
GGGRGAGGVG VSTGTFNNQT EFQYLGEGLV RITAHASRLI HLNMPEHETY KRIHVLNSES
GVAGQMVQDD AHTQMVTPWS LIDANAWGVW FNPADWQLIS NNMTEINLVS FEQEIFNVVL
KTITESATSP PTKIYNNDLT ASLMVALDTN NTLPYTPAAP RSETLGFYPW LPTKPTQYRY
YLSCIRNLNP PTYTGQSQQI TDSIQTGLHS DIMFYTIENA VPIHLLRTGD EFSTGIYHFD
TKPLKLTHSW QTNRSLGLPP KLLTEPTTEG DQHPGTLPAA NTRKGYHQTI NNSYTEATAI
RPAQVGYNTP YMNFEYSNGG PFLTPIVPTA DTQYNDDEPN GAIRFTMDYQ HGHLTTSSQE
LERYTFNPQS KCGRAPKQQF NQQAPLNLEN TNNGTLLPSD PIGGKSNMHF MNTLNTYGPL
TALNNTAPVF PNGQIWDKEL DTDLKPRLHV TAPFVCKNNP PGQLFVKIAP NLTDDFNADS
PQQPRIITYS NFWWKGTLTF TAKMRSSNMW NPIQQHTTTA ENIGNYIPTN IGGIRMFPEY
SQLIPRKLY
