ID CAPSD_NODAM Reviewed; 399 AA. AC P12871; Q9IMM2; DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot. DT 01-OCT-1989, sequence version 1. DT 08-NOV-2023, entry version 134. 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 Nodamura virus (strain Mag115) (NoV). OC Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Magsaviricetes; OC Nodamuvirales; Nodaviridae; Alphanodavirus; Nodamura virus. OX NCBI_TaxID=914672; OH NCBI_TaxID=7158; Aedes. OH NCBI_TaxID=7088; Lepidoptera (butterflies and moths). OH NCBI_TaxID=9823; Sus scrofa (Pig). RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC RNA]. RX PubMed=2798110; DOI=10.1093/nar/17.18.7525; RA Dasgupta R., Sgro J.-Y.; RT "Nucleotide sequences of three Nodavirus RNA2's: the messengers for their RT coat protein precursors."; RL Nucleic Acids Res. 17:7525-7526(1989). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC RNA]. RX PubMed=12573589; DOI=10.1006/viro.2002.1769; RA Johnson K.L., Price B.D., Ball L.A.; RT "Recovery of infectivity from cDNA clones of nodamura virus and RT identification of small nonstructural proteins."; RL Virology 305:436-451(2003). RN [3] RP SIMILARITY TO OTHER NODAVIRUSES. RX PubMed=2116525; DOI=10.1016/0022-2836(90)90191-n; RA Kaesberg P., Dasgupta R., Sgro J.-Y., Wery J.-P., Selling B.H., Hosur M.V., RA Johnson J.E.; RT "Structural homology among four nodaviruses as deduced by sequencing and X- RT ray crystallography."; RL J. Mol. Biol. 214:423-435(1990). RN [4] RP X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS). RX PubMed=15299863; DOI=10.1107/s0907444997007427; RA Zlotnick A., Natarajan P., Munshi S., Johnson J.E.; RT "Resolution of space-group ambiguity and the structure determination of RT nodamura virus to 3.3-A resolution from pseudo-R32 (monoclinic) crystals."; RL Acta Crystallogr. D 53:738-746(1997). 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 -!- 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=1nov"; 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; X15961; CAA34083.1; -; Genomic_RNA. DR EMBL; AF174534; AAF97862.1; -; Genomic_RNA. DR PIR; C34011; VCBBND. DR RefSeq; NP_077732.1; NC_002691.1. DR PDB; 1NOV; X-ray; 3.50 A; A/B/C=1-355, D/E/F=356-399. DR PDBsum; 1NOV; -. DR SMR; P12871; -. DR MEROPS; N01.001; -. DR TCDB; 1.A.61.1.1; the insect nodavirus channel-forming chain f (gamma-peptide) family. DR KEGG; vg:962119; -. DR EvolutionaryTrace; P12871; -. DR Proteomes; UP000166289; 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; Reference proteome; KW T=3 icosahedral capsid protein; Viral penetration into host cytoplasm; KW Viral penetration via permeabilization of host membrane; Virion; KW Virus entry into host cell. FT CHAIN 1..399 FT /note="Capsid protein alpha" FT /id="PRO_0000402389" FT CHAIN 1..355 FT /note="Capsid protein beta" FT /id="PRO_0000039196" FT CHAIN 356..399 FT /note="Membrane-lytic peptide gamma" FT /id="PRO_0000039197" FT REGION 1..46 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 25..39 FT /note="Basic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT ACT_SITE 67 FT /evidence="ECO:0000250|UniProtKB:P12870" FT BINDING 216 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="2" FT /evidence="ECO:0000250|UniProtKB:P12870" FT BINDING 216 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="3" FT /evidence="ECO:0000250|UniProtKB:P12870" FT BINDING 216 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="4" FT /evidence="ECO:0000250|UniProtKB:P12870" FT BINDING 244 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="5" FT /evidence="ECO:0000250|UniProtKB:P12870" FT BINDING 246 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="5" FT /evidence="ECO:0000250|UniProtKB:P12870" FT SITE 355..356 FT /note="Cleavage; by autolysis" FT /evidence="ECO:0000250|UniProtKB:P12870" FT DISULFID 61..310 FT CONFLICT 279 FT /note="R -> A (in Ref. 2; AAF97862)" FT /evidence="ECO:0000305" FT CONFLICT 393 FT /note="T -> A (in Ref. 2; AAF97862)" FT /evidence="ECO:0000305" FT HELIX 11..15 FT /evidence="ECO:0007829|PDB:1NOV" FT HELIX 53..63 FT /evidence="ECO:0007829|PDB:1NOV" FT HELIX 65..67 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 68..70 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 82..97 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 101..107 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 113..121 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 131..135 FT /evidence="ECO:0007829|PDB:1NOV" FT HELIX 139..142 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 152..160 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 163..168 FT /evidence="ECO:0007829|PDB:1NOV" FT TURN 172..174 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 178..184 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 188..197 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 199..201 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 203..213 FT /evidence="ECO:0007829|PDB:1NOV" FT HELIX 215..219 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 226..229 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 234..237 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 242..244 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 255..258 FT /evidence="ECO:0007829|PDB:1NOV" FT TURN 264..268 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 276..278 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 288..295 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 301..315 FT /evidence="ECO:0007829|PDB:1NOV" FT STRAND 319..321 FT /evidence="ECO:0007829|PDB:1NOV" FT HELIX 333..345 FT /evidence="ECO:0007829|PDB:1NOV" FT HELIX 358..369 FT /evidence="ECO:0007829|PDB:1NOV" FT HELIX 370..372 FT /evidence="ECO:0007829|PDB:1NOV" SQ SEQUENCE 399 AA; 43067 MW; A026158C6548060B CRC64; MVSKAARRRR AAPRQQQRQQ SNRASNQPRR RRARRTRRQQ RMAATNNMLK MSAPGLDFLK CAFASPDFST DPGKGIPDKF QGLVLPKKHC LTQSITFTPG KQTMLLVAPI PGIACLKAEA NVGASFSGVP LASVEFPGFD QLFGTSATDT AANVTAFRYA SMAAGVYPTS NLMQFAGSIQ VYKIPLKQVL NSYSQTVATV PPTNLAQNTI AIDGLEALDA LPNNNYSGSF IEGCYSQSVC NEPEFEFHPI MEGYASVPPA NVTNAQASMF TNLTFSGARY TGLGDMDAIA ILVTTPTGAV NTAVLKVWAC VEYRPNPNST LYEFARESPA NDEYALAAYR KIARDIPIAV ACKDNATFWE RVRSILKSGL NFASTIPGPV GVAATGIKGI IETIGSLWV //