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 28-JUN-2023, entry version 107. DE RecName: Full=Capsid protein alpha; DE EC=3.4.23.44 {ECO:0000250|UniProtKB:P12870}; DE Contains: DE RecName: Full=Capsid protein beta; DE AltName: Full=Coat protein beta; DE AltName: Full=Nodavirus endopeptidase; DE Contains: DE RecName: Full=Membrane-lytic 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]: Capsid protein alpha self-assembles CC to form an icosahedral procapsid with a T=3 symmetry, about 30 nm in CC diameter, and consisting of 60 capsid proteins trimers. In addition, CC 240 calcium ions are incorporated per capsid during assembly. The CC capsid encapsulates the two genomic RNAs. Capsid maturation occurs via CC autoproteolytic cleavage of capsid protein alpha generating capsid CC protein beta and the membrane-active peptide gamma. CC {ECO:0000250|UniProtKB:P12870}. CC -!- FUNCTION: [Membrane-lytic peptide gamma]: Membrane-permeabilizing CC peptide produced by virus maturation, thereby creating the infectious CC virion. After endocytosis into the host cell, peptide gamma is probably CC exposed in endosomes, where it permeabilizes the endosomal membrane, CC facilitating translocation of viral capsid or RNA into the cytoplasm. CC Involved in specific recognition and packaging of viral RNA during CC assembly. {ECO:0000250|UniProtKB:P12870}. CC -!- CATALYTIC ACTIVITY: [Capsid protein beta]: 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; Evidence={ECO:0000250|UniProtKB:P12870}; CC -!- SUBCELLULAR LOCATION: [Capsid protein beta]: Virion {ECO:0000305}. CC -!- SUBCELLULAR LOCATION: [Membrane-lytic peptide gamma]: Virion CC {ECO:0000305}. Note=located inside the capsid. {ECO:0000305}. CC -!- PTM: [Capsid protein alpha]: Capsid protein alpha autocatalytically CC maturates into capsid protein beta and peptide gamma. CC {ECO:0000250|UniProtKB:P12870}. CC -!- MASS SPECTROMETRY: [Membrane-lytic peptide gamma]: Mass=4246; CC Method=MALDI; 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"; CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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 OrthoDB; 10195at10239; -. 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. DR SUPFAM; SSF88633; Positive stranded ssRNA viruses; 1. 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="Membrane-lytic 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|UniProtKB:P12870" FT BINDING 249 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:P12870" FT BINDING 251 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:P12870" FT BINDING 272 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="1" FT /evidence="ECO:0000250|UniProtKB:P12870" FT BINDING 272 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="3" FT /evidence="ECO:0000250|UniProtKB:P12870" FT SITE 361..362 FT /note="Cleavage; by autolysis" FT /evidence="ECO:0000250|UniProtKB:P12870" 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 //