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P12871

- CAPSD_NODAM

UniProt

P12871 - CAPSD_NODAM

Protein

Capsid protein alpha

Gene

alpha

Organism
Nodamura virus (strain Mag115) (NoV)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 102 (01 Oct 2014)
      Sequence version 1 (01 Oct 1989)
      Previous versions | rss
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    Functioni

    Capsid protein alpha self-assembles to form an icosahedral procapsid with a T=3 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins trimers. The capsid encapsulates the two genomic RNAs. Capsid maturation occurs via autoproteolytic cleavage of capsid protein alpha generating capsid protein beta and the membrane-active peptide gamma By similarity.By similarity
    Peptide gamma: membrane-permeabilizing peptide produced by virus maturation, thereby creating the infectious virion. After endocytosis into the host cell, peptide gamma is probably exposed in endosomes, where it permeabilizes the endosomal membrane, facilitating translocation of viral capsid or RNA into the cytoplasm By similarity.By similarity

    Catalytic activityi

    Hydrolysis of an asparaginyl bond involved in the maturation of the structural protein of the virus, typically -Asn-|-Ala- or -Asn-|-Phe-.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei67 – 671By similarity

    GO - Molecular functioni

    1. aspartic-type endopeptidase activity Source: UniProtKB-KW

    GO - Biological processi

    1. permeabilization of host organelle membrane involved in viral entry into host cell Source: UniProtKB-KW

    Keywords - Molecular functioni

    Aspartyl protease, Hydrolase, Protease

    Keywords - Biological processi

    Viral penetration into host cytoplasm, Viral penetration via permeabilization of host membrane, Virus entry into host cell

    Protein family/group databases

    MEROPSiN01.001.
    TCDBi1.A.61.1.1. the insect nodavirus channel-forming chain f (gamma-peptide) family.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Capsid protein alpha
    Cleaved into the following 2 chains:
    Alternative name(s):
    Coat protein beta
    Nodavirus endopeptidase
    Alternative name(s):
    Coat protein gamma
    Gene namesi
    Name:alpha
    OrganismiNodamura virus (strain Mag115) (NoV)
    Taxonomic identifieri914672 [NCBI]
    Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageNodaviridaeAlphanodavirus
    Virus hostiAedes [TaxID: 7158]
    Lepidoptera (butterflies and moths) [TaxID: 7088]
    Sus scrofa (Pig) [TaxID: 9823]
    ProteomesiUP000008594: Genome

    Subcellular locationi

    Chain Peptide gamma : Virion Curated
    Note: located inside the capsid.Curated

    GO - Cellular componenti

    1. T=3 icosahedral viral capsid Source: UniProtKB-KW

    Keywords - Cellular componenti

    Capsid protein, T=3 icosahedral capsid protein, Virion

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 399399Capsid protein alphaPRO_0000402389Add
    BLAST
    Chaini1 – 355355Capsid protein betaPRO_0000039196Add
    BLAST
    Chaini356 – 39944Peptide gammaPRO_0000039197Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi61 ↔ 310

    Post-translational modificationi

    Capsid protein alpha autocatalytically maturates into capsid protein beta and peptide gamma.By similarity

    Keywords - PTMi

    Disulfide bond

    Structurei

    Secondary structure

    1
    399
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi53 – 6311
    Helixi65 – 673
    Beta strandi68 – 703
    Beta strandi82 – 9716
    Beta strandi101 – 1077
    Beta strandi113 – 1219
    Beta strandi131 – 1355
    Helixi139 – 1424
    Beta strandi152 – 1609
    Beta strandi163 – 1686
    Turni172 – 1743
    Beta strandi178 – 1847
    Beta strandi188 – 19710
    Beta strandi199 – 2013
    Beta strandi203 – 21311
    Helixi215 – 2195
    Beta strandi226 – 2294
    Beta strandi234 – 2374
    Beta strandi242 – 2443
    Beta strandi255 – 2584
    Turni264 – 2685
    Beta strandi276 – 2783
    Beta strandi288 – 2958
    Beta strandi301 – 31515
    Beta strandi319 – 3213
    Helixi333 – 34513
    Helixi358 – 36912
    Helixi370 – 3723

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1NOVX-ray3.50A/B/C1-355[»]
    D/E/F356-399[»]
    ProteinModelPortaliP12871.
    SMRiP12871. Positions 19-355.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP12871.

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi7 – 104Poly-Arg
    Compositional biasi29 – 3810Poly-Arg

    Sequence similaritiesi

    Belongs to the peptidase A6 family.Curated

    Family and domain databases

    Gene3Di2.60.120.20. 1 hit.
    InterProiIPR000696. Peptidase_A6.
    IPR029053. Viral_coat.
    [Graphical view]
    PfamiPF01829. Peptidase_A6. 1 hit.
    [Graphical view]
    PRINTSiPR00863. NODAVIRPTASE.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P12871-1 [UniParc]FASTAAdd to Basket

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    MVSKAARRRR AAPRQQQRQQ SNRASNQPRR RRARRTRRQQ RMAATNNMLK    50
    MSAPGLDFLK CAFASPDFST DPGKGIPDKF QGLVLPKKHC LTQSITFTPG 100
    KQTMLLVAPI PGIACLKAEA NVGASFSGVP LASVEFPGFD QLFGTSATDT 150
    AANVTAFRYA SMAAGVYPTS NLMQFAGSIQ VYKIPLKQVL NSYSQTVATV 200
    PPTNLAQNTI AIDGLEALDA LPNNNYSGSF IEGCYSQSVC NEPEFEFHPI 250
    MEGYASVPPA NVTNAQASMF TNLTFSGARY TGLGDMDAIA ILVTTPTGAV 300
    NTAVLKVWAC VEYRPNPNST LYEFARESPA NDEYALAAYR KIARDIPIAV 350
    ACKDNATFWE RVRSILKSGL NFASTIPGPV GVAATGIKGI IETIGSLWV 399
    Length:399
    Mass (Da):43,067
    Last modified:October 1, 1989 - v1
    Checksum:iA026158C6548060B
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti279 – 2791R → A in AAF97862. 1 PublicationCurated
    Sequence conflicti393 – 3931T → A in AAF97862. 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X15961 Genomic RNA. Translation: CAA34083.1.
    AF174534 Genomic RNA. Translation: AAF97862.1.
    PIRiC34011. VCBBND.

    Cross-referencesi

    Web resourcesi

    Virus Particle ExploreR db

    Icosahedral capsid structure

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X15961 Genomic RNA. Translation: CAA34083.1 .
    AF174534 Genomic RNA. Translation: AAF97862.1 .
    PIRi C34011. VCBBND.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1NOV X-ray 3.50 A/B/C 1-355 [» ]
    D/E/F 356-399 [» ]
    ProteinModelPortali P12871.
    SMRi P12871. Positions 19-355.
    ModBasei Search...
    MobiDBi Search...

    Protein family/group databases

    MEROPSi N01.001.
    TCDBi 1.A.61.1.1. the insect nodavirus channel-forming chain f (gamma-peptide) family.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei P12871.

    Family and domain databases

    Gene3Di 2.60.120.20. 1 hit.
    InterProi IPR000696. Peptidase_A6.
    IPR029053. Viral_coat.
    [Graphical view ]
    Pfami PF01829. Peptidase_A6. 1 hit.
    [Graphical view ]
    PRINTSi PR00863. NODAVIRPTASE.
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequences of three Nodavirus RNA2's: the messengers for their coat protein precursors."
      Dasgupta R., Sgro J.-Y.
      Nucleic Acids Res. 17:7525-7526(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    2. "Complete genome sequence of Nodamura virus derived from functional cDNA clones."
      Johnson K.L., Ball L.A.
      Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    3. "Structural homology among four nodaviruses as deduced by sequencing and X-ray crystallography."
      Kaesberg P., Dasgupta R., Sgro J.-Y., Wery J.-P., Selling B.H., Hosur M.V., Johnson J.E.
      J. Mol. Biol. 214:423-435(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: SIMILARITY TO OTHER NODAVIRUSES.
    4. "Resolution of space-group ambiguity and the structure determination of nodamura virus to 3.3-A resolution from pseudo-R32 (monoclinic) crystals."
      Zlotnick A., Natarajan P., Munshi S., Johnson J.E.
      Acta Crystallogr. D 53:738-746(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS).

    Entry informationi

    Entry nameiCAPSD_NODAM
    AccessioniPrimary (citable) accession number: P12871
    Secondary accession number(s): Q9IMM2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: October 1, 1989
    Last modified: October 1, 2014
    This is version 102 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. Peptidase families
      Classification of peptidase families and list of entries
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3