CAPSD_PAV
ID CAPSD_PAV Reviewed; 401 AA.
AC Q9J7Z0;
DT 16-APR-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 105.
DE RecName: Full=Capsid protein alpha;
DE Contains:
DE RecName: Full=Capsid protein beta;
DE EC=3.4.23.44;
DE AltName: Full=Coat protein beta;
DE AltName: Full=Nodavirus endopeptidase;
DE Contains:
DE RecName: Full=Peptide gamma;
DE AltName: Full=Coat protein gamma;
GN Name=alpha;
OS Pariacoto virus (PaV).
OC Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Magsaviricetes;
OC Nodamuvirales; Nodaviridae; Alphanodavirus.
OX NCBI_TaxID=103782;
OH NCBI_TaxID=37547; Spodoptera eridania (Southern armyworm).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC RNA], AND MASS SPECTROMETRY.
RX PubMed=10799587; DOI=10.1128/jvi.74.11.5123-5132.2000;
RA Johnson K.N., Zeddam J.-L., Ball L.A.;
RT "Characterization and construction of functional cDNA clones of Pariacoto
RT virus, the first Alphanodavirus isolated outside Australasia.";
RL J. Virol. 74:5123-5132(2000).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 7-401.
RX PubMed=11135676; DOI=10.1038/83089;
RA Tang L., Johnson K.N., Ball L.A., Lin T., Yeager M., Johnson J.E.;
RT "The structure of pariacoto virus reveals a dodecahedral cage of duplex
RT RNA.";
RL Nat. Struct. Biol. 8:77-83(2001).
CC -!- FUNCTION: Capsid protein alpha self-assembles to form an icosahedral
CC procapsid with a T=3 symmetry, about 30 nm in diameter, and consisting
CC of 60 capsid proteins trimers. In addition, calcium ions are
CC incorporated per capsid during assembly. The capsid encapsulates the
CC two genomic RNAs. Capsid maturation occurs via autoproteolytic cleavage
CC of capsid protein alpha generating capsid protein beta and the
CC membrane-active peptide gamma (By similarity). {ECO:0000250}.
CC -!- FUNCTION: [Peptide gamma]: Membrane-permeabilizing peptide produced by
CC virus maturation, thereby creating the infectious virion. After
CC endocytosis into the host cell, peptide gamma is probably exposed in
CC endosomes, where it permeabilizes the endosomal membrane, facilitating
CC translocation of viral capsid or RNA into the cytoplasm (By
CC similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of an asparaginyl bond involved in the maturation
CC of the structural protein of the virus, typically -Asn-|-Ala- or
CC -Asn-|-Phe-.; EC=3.4.23.44;
CC -!- SUBCELLULAR LOCATION: [Capsid protein beta]: Virion {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: [Peptide gamma]: Virion {ECO:0000305}.
CC Note=located inside the capsid. {ECO:0000305}.
CC -!- PTM: Capsid protein alpha autocatalytically maturates into capsid
CC protein beta and peptide gamma. {ECO:0000250}.
CC -!- MASS SPECTROMETRY: [Peptide gamma]: Mass=4246; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:10799587};
CC -!- SIMILARITY: Belongs to the peptidase A6 family. {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=1f8v";
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DR EMBL; AF171943; AAF71693.1; -; Genomic_RNA.
DR RefSeq; NP_620111.1; NC_003692.1.
DR PDB; 1F8V; X-ray; 3.00 A; A/B/C=7-361, D/E/F=362-401.
DR PDBsum; 1F8V; -.
DR SMR; Q9J7Z0; -.
DR GeneID; 956349; -.
DR KEGG; vg:956349; -.
DR EvolutionaryTrace; Q9J7Z0; -.
DR Proteomes; UP000204174; Genome.
DR GO; GO:0039617; C:T=3 icosahedral viral capsid; IEA:UniProtKB-KW.
DR GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; 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:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0099008; P:viral entry via permeabilization of inner membrane; IEA:UniProtKB-KW.
DR Gene3D; 2.60.120.20; -; 1.
DR InterPro; IPR000696; Peptidase_A6.
DR InterPro; IPR029053; Viral_coat.
DR Pfam; PF01829; Peptidase_A6; 1.
DR PRINTS; PR00863; NODAVIRPTASE.
PE 1: Evidence at protein level;
KW 3D-structure; Aspartyl protease; Calcium; Capsid protein; Disulfide bond;
KW Hydrolase; Metal-binding; Protease; T=3 icosahedral capsid protein;
KW Viral penetration into host cytoplasm;
KW Viral penetration via permeabilization of host membrane; Virion;
KW Virus entry into host cell.
FT CHAIN 1..401
FT /note="Capsid protein alpha"
FT /id="PRO_0000402390"
FT CHAIN 1..361
FT /note="Capsid protein beta"
FT /id="PRO_0000039198"
FT CHAIN 362..401
FT /note="Peptide gamma"
FT /id="PRO_0000039199"
FT REGION 1..43
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..15
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 68
FT /evidence="ECO:0000250"
FT BINDING 249
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT BINDING 251
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT DISULFID 62..316
FT /evidence="ECO:0000250"
FT TURN 20..22
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:1F8V"
FT HELIX 54..64
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 68..71
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 83..98
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 100..108
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 114..121
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 129..134
FT /evidence="ECO:0007829|PDB:1F8V"
FT HELIX 138..142
FT /evidence="ECO:0007829|PDB:1F8V"
FT TURN 146..149
FT /evidence="ECO:0007829|PDB:1F8V"
FT TURN 151..153
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 155..170
FT /evidence="ECO:0007829|PDB:1F8V"
FT TURN 174..176
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 180..186
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 189..200
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 207..218
FT /evidence="ECO:0007829|PDB:1F8V"
FT HELIX 219..221
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 223..225
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 228..234
FT /evidence="ECO:0007829|PDB:1F8V"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 239..242
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 247..249
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 256..266
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 274..276
FT /evidence="ECO:0007829|PDB:1F8V"
FT HELIX 278..281
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 294..301
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 307..321
FT /evidence="ECO:0007829|PDB:1F8V"
FT HELIX 328..330
FT /evidence="ECO:0007829|PDB:1F8V"
FT HELIX 339..348
FT /evidence="ECO:0007829|PDB:1F8V"
FT HELIX 363..374
FT /evidence="ECO:0007829|PDB:1F8V"
FT STRAND 379..381
FT /evidence="ECO:0007829|PDB:1F8V"
SQ SEQUENCE 401 AA; 43326 MW; 1E518977DE7A2C90 CRC64;
MVSRTKNRRN KARKVVSRST ALVPMAPASQ RTGPAPRKPR KRNQALVRNP RLTDAGLAFL
KCAFAAPDFS VDPGKGIPDN FHGRTLAIKD CNTTSVVFTP NTDTYIVVAP VPGFAYFRAE
VAVGAQPTTF VGVPYPTYAT NFGAGSQNGL PAVNNYSKFR YASMACGLYP TSNMMQFSGS
VQVWRVDLNL SEAVNPAVTA ITPAPGVFAN FVDKRINGLR GIRPLAPRDN YSGNFIDGAY
TFAFDKSTDF EWCDFVRSLE FSESNVLGAA TAMKLLAPGG GTDTTLTGLG NVNTLVYKIS
TPTGAVNTAI LRTWNCIELQ PYTDSALFQF SGVSPPFDPL ALECYHNLKM RFPVAVSSRE
NSKFWEGVLR VLNQISGTLS VIPGPVGTIS AGVHQLTGMY M
