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P12870

- CAPSD_FHV

UniProt

P12870 - CAPSD_FHV

Protein

Capsid protein alpha

Gene

alpha

Organism
Flock house virus (FHV)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 91 (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. In addition, 240 calcium ions are incorporated per capsid during assembly. 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.
    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 Probable.Curated

    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 sitei75 – 751By similarity
    Metal bindingi249 – 2491Calcium
    Metal bindingi251 – 2511Calcium

    GO - Molecular functioni

    1. aspartic-type endopeptidase activity Source: UniProtKB-KW
    2. metal ion binding 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

    Keywords - Ligandi

    Calcium, Metal-binding

    Protein family/group databases

    MEROPSiN01.001.

    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
    OrganismiFlock house virus (FHV)
    Taxonomic identifieri12287 [NCBI]
    Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageNodaviridaeAlphanodavirus
    Virus hostiCostelytra zealandica [TaxID: 50579]
    Galleria mellonella (Greater wax moth) [TaxID: 7137]
    Hordeum vulgare (Barley) [TaxID: 4513]
    Saccharomyces cerevisiae (Baker's yeast) [TaxID: 4932]

    Subcellular locationi

    Chain Peptide gamma : Virion Curated
    Note: Located inside the capsid and probably externalized in early endosomes.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 – 407407Capsid protein alphaPRO_0000402388Add
    BLAST
    Chaini1 – 363363Capsid protein betaPRO_0000039194Add
    BLAST
    Chaini364 – 40744Peptide gammaPRO_0000039195Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi69 ↔ 318

    Post-translational modificationi

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

    Keywords - PTMi

    Disulfide bond

    Structurei

    Secondary structure

    1
    407
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi61 – 7111
    Beta strandi76 – 783
    Beta strandi90 – 10516
    Beta strandi109 – 1157
    Beta strandi121 – 1299
    Beta strandi139 – 1446
    Helixi148 – 1525
    Beta strandi161 – 17717
    Turni181 – 1833
    Beta strandi187 – 1937
    Beta strandi196 – 2049
    Beta strandi210 – 21910
    Helixi220 – 2245
    Beta strandi228 – 2347
    Helixi235 – 2373
    Beta strandi239 – 2424
    Beta strandi247 – 2493
    Beta strandi260 – 2634
    Helixi269 – 2724
    Beta strandi275 – 2795
    Turni283 – 2853
    Beta strandi296 – 3027
    Beta strandi309 – 32315
    Helixi329 – 3324
    Helixi341 – 35313
    Beta strandi356 – 3583
    Helixi360 – 3623
    Helixi367 – 37913

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3LOBX-ray3.60A/B/C1-363[»]
    D/E/F364-407[»]
    4FSJX-ray3.50A/B/C1-363[»]
    D/E/F364-407[»]
    4FTBX-ray2.70A/B/C1-363[»]
    D/E/F364-407[»]
    4FTEX-ray3.50A/B/C1-407[»]
    4FTSX-ray3.20A/B/C1-407[»]
    ProteinModelPortaliP12870.
    SMRiP12870. Positions 19-363.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP12870.

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi35 – 4915Poly-ArgAdd
    BLAST

    Sequence similaritiesi

    Belongs to the peptidase A6 family.Curated

    Family and domain databases

    Gene3Di2.60.120.20. 1 hit.
    4.10.180.10. 1 hit.
    InterProiIPR027440. Capsid_prot_alpha-like_dom.
    IPR000696. 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.

    P12870-1 [UniParc]FASTAAdd to Basket

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    MVNNNRPRRQ RAQRVVVTTT QTAPVPQQNV PRNGRRRRNR TRRNRRRVRG    50
    MNMAALTRLS QPGLAFLKCA FAPPDFNTDP GKGIPDRFEG KVVSRKDVLN 100
    QSISFTAGQD TFILIAPTPG VAYWSASVPA GTFPTSATTF NPVNYPGFTS 150
    MFGTTSTSRS DQVSSFRYAS MNVGIYPTSN LMQFAGSITV WKCPVKLSTV 200
    QFPVATDPAT SSLVHTLVGL DGVLAVGPDN FSESFIKGVF SQSACNEPDF 250
    EFNDILEGIQ TLPPANVSLG STGQPFTMDS GAEATSGVVG WGNMDTIVIR 300
    VSAPEGAVNS AILKAWSCIE YRPNPNAMLY QFGHDSPPLD EVALQEYRTV 350
    ARSLPVAVIA AQNASMWERV KSIIKSSLAA ASNIPGPIGV AASGISGLSA 400
    LFEGFGF 407
    Length:407
    Mass (Da):43,710
    Last modified:October 1, 1989 - v1
    Checksum:i5A66E01BAD2FEB0B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X15959 Genomic RNA. Translation: CAA34081.1.
    PIRiB34011. VCBBFH.
    RefSeqiNP_689442.1. NC_004144.1.

    Genome annotation databases

    GeneIDi962115.

    Cross-referencesi

    Web resourcesi

    Virus Particle ExploreR db

    Icosahedral capsid structure

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X15959 Genomic RNA. Translation: CAA34081.1 .
    PIRi B34011. VCBBFH.
    RefSeqi NP_689442.1. NC_004144.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3LOB X-ray 3.60 A/B/C 1-363 [» ]
    D/E/F 364-407 [» ]
    4FSJ X-ray 3.50 A/B/C 1-363 [» ]
    D/E/F 364-407 [» ]
    4FTB X-ray 2.70 A/B/C 1-363 [» ]
    D/E/F 364-407 [» ]
    4FTE X-ray 3.50 A/B/C 1-407 [» ]
    4FTS X-ray 3.20 A/B/C 1-407 [» ]
    ProteinModelPortali P12870.
    SMRi P12870. Positions 19-363.
    ModBasei Search...
    MobiDBi Search...

    Protein family/group databases

    MEROPSi N01.001.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 962115.

    Miscellaneous databases

    EvolutionaryTracei P12870.

    Family and domain databases

    Gene3Di 2.60.120.20. 1 hit.
    4.10.180.10. 1 hit.
    InterProi IPR027440. Capsid_prot_alpha-like_dom.
    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. "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.
    3. "Specific encapsidation of nodavirus RNAs is mediated through the C terminus of capsid precursor protein alpha."
      Schneemann A., Marshall D.
      J. Virol. 72:8738-8746(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF PEPTIDE GAMMA.
    4. "Low endocytic pH and capsid protein autocleavage are critical components of Flock House virus cell entry."
      Odegard A.L., Kwan M.H., Walukiewicz H.E., Banerjee M., Schneemann A., Johnson J.E.
      J. Virol. 83:8628-8637(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION OF PEPTIDE GAMMA, PROTEOLYTIC PROCESSING OF POLYPROTEIN.
    5. "Ordered duplex RNA controls capsid architecture in an icosahedral animal virus."
      Fisher A.J., Johnson J.E.
      Nature 361:176-179(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS).
    6. "Structure and function of a genetically engineered mimic of a nonenveloped virus entry intermediate."
      Banerjee M., Speir J.A., Kwan M.H., Huang R., Aryanpur P.P., Bothner B., Johnson J.E.
      J. Virol. 84:4737-4746(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.6 ANGSTROMS), FUNCTION.

    Entry informationi

    Entry nameiCAPSD_FHV
    AccessioniPrimary (citable) accession number: P12870
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: October 1, 1989
    Last modified: October 1, 2014
    This is version 91 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

    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