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P12870 (CAPSD_FHV) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 87. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Capsid protein alpha

Cleaved into the following 2 chains:

  1. Capsid protein beta
    EC=3.4.23.44
    Alternative name(s):
    Coat protein beta
    Nodavirus endopeptidase
  2. Peptide gamma
    Alternative name(s):
    Coat protein gamma
Gene names
Name:alpha
OrganismFlock house virus (FHV)
Taxonomic identifier12287 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageNodaviridaeAlphanodavirus
Virus hostCostelytra zealandica [TaxID: 50579]
Galleria mellonella (Greater wax moth) [TaxID: 7137]
Hordeum vulgare (Barley) [TaxID: 4513]
Saccharomyces cerevisiae (Baker's yeast) [TaxID: 4932]

Protein attributes

Sequence length407 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.3 Ref.4 Ref.6

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. Ref.3 Ref.4 Ref.6

Catalytic activity

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

Subcellular location

Capsid protein beta: Virion Potential.

Peptide gamma: Virion Potential. Note: Located inside the capsid and probably externalized in early endosomes Potential.

Post-translational modification

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

Sequence similarities

Belongs to the peptidase A6 family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 407407Capsid protein alpha
PRO_0000402388
Chain1 – 363363Capsid protein beta
PRO_0000039194
Chain364 – 40744Peptide gamma
PRO_0000039195

Regions

Compositional bias35 – 4915Poly-Arg

Sites

Active site751 By similarity
Metal binding2491Calcium
Metal binding2511Calcium

Amino acid modifications

Disulfide bond69 ↔ 318

Secondary structure

....................................................... 407
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P12870 [UniParc].

Last modified October 1, 1989. Version 1.
Checksum: 5A66E01BAD2FEB0B

FASTA40743,710
        10         20         30         40         50         60 
MVNNNRPRRQ RAQRVVVTTT QTAPVPQQNV PRNGRRRRNR TRRNRRRVRG MNMAALTRLS 

        70         80         90        100        110        120 
QPGLAFLKCA FAPPDFNTDP GKGIPDRFEG KVVSRKDVLN QSISFTAGQD TFILIAPTPG 

       130        140        150        160        170        180 
VAYWSASVPA GTFPTSATTF NPVNYPGFTS MFGTTSTSRS DQVSSFRYAS MNVGIYPTSN 

       190        200        210        220        230        240 
LMQFAGSITV WKCPVKLSTV QFPVATDPAT SSLVHTLVGL DGVLAVGPDN FSESFIKGVF 

       250        260        270        280        290        300 
SQSACNEPDF EFNDILEGIQ TLPPANVSLG STGQPFTMDS GAEATSGVVG WGNMDTIVIR 

       310        320        330        340        350        360 
VSAPEGAVNS AILKAWSCIE YRPNPNAMLY QFGHDSPPLD EVALQEYRTV ARSLPVAVIA 

       370        380        390        400 
AQNASMWERV KSIIKSSLAA ASNIPGPIGV AASGISGLSA LFEGFGF 

« Hide

References

[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.

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X15959 Genomic RNA. Translation: CAA34081.1.
PIRVCBBFH. B34011.
RefSeqNP_689442.1. NC_004144.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalP12870.
SMRP12870. Positions 19-363.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

MEROPSN01.001.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID962115.

Family and domain databases

Gene3D4.10.180.10. 1 hit.
InterProIPR027440. Capsid_prot_alpha-like_dom.
IPR000696. Peptidase_A6.
[Graphical view]
PfamPF01829. Peptidase_A6. 1 hit.
[Graphical view]
PRINTSPR00863. NODAVIRPTASE.
ProtoNetSearch...

Other

EvolutionaryTraceP12870.

Entry information

Entry nameCAPSD_FHV
AccessionPrimary (citable) accession number: P12870
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: February 19, 2014
This is version 87 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references