CAPSD_NODAM
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 03-AUG-2022, entry version 130.
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 Nodamura virus (strain Mag115) (NoV).
OC Viruses; Riboviria; Orthornavirae; Kitrinoviricota; Magsaviricetes;
OC Nodamuvirales; Nodaviridae; Alphanodavirus.
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 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. The capsid encapsulates the two genomic
CC RNAs. Capsid maturation occurs via autoproteolytic cleavage of capsid
CC protein alpha generating capsid protein beta and the membrane-active
CC 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 -!- 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 GeneID; 962119; -.
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: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; Capsid protein; Disulfide bond; Hydrolase;
KW Protease; Reference proteome; 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..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="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"
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
