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P12871 (CAPSD_NODAM) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 98. 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
OrganismNodamura virus (strain Mag115) (NoV) [Reference proteome]
Taxonomic identifier914672 [NCBI]
Taxonomic lineageVirusesssRNA positive-strand viruses, no DNA stageNodaviridaeAlphanodavirus
Virus hostAedes [TaxID: 7158]
Lepidoptera (butterflies and moths) [TaxID: 7088]
Sus scrofa (Pig) [TaxID: 9823]

Protein attributes

Sequence length399 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. 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.

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.

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 Potential.

Post-translational modification

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

Sequence similarities

Belongs to the peptidase A6 family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 399399Capsid protein alpha
PRO_0000402389
Chain1 – 355355Capsid protein beta
PRO_0000039196
Chain356 – 39944Peptide gamma
PRO_0000039197

Regions

Compositional bias7 – 104Poly-Arg
Compositional bias29 – 3810Poly-Arg

Sites

Active site671 By similarity

Amino acid modifications

Disulfide bond61 ↔ 310

Experimental info

Sequence conflict2791R → A in AAF97862. Ref.2
Sequence conflict3931T → A in AAF97862. Ref.2

Secondary structure

....................................................... 399
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P12871 [UniParc].

Last modified October 1, 1989. Version 1.
Checksum: A026158C6548060B

FASTA39943,067
        10         20         30         40         50         60 
MVSKAARRRR AAPRQQQRQQ SNRASNQPRR RRARRTRRQQ RMAATNNMLK MSAPGLDFLK 

        70         80         90        100        110        120 
CAFASPDFST DPGKGIPDKF QGLVLPKKHC LTQSITFTPG KQTMLLVAPI PGIACLKAEA 

       130        140        150        160        170        180 
NVGASFSGVP LASVEFPGFD QLFGTSATDT AANVTAFRYA SMAAGVYPTS NLMQFAGSIQ 

       190        200        210        220        230        240 
VYKIPLKQVL NSYSQTVATV PPTNLAQNTI AIDGLEALDA LPNNNYSGSF IEGCYSQSVC 

       250        260        270        280        290        300 
NEPEFEFHPI MEGYASVPPA NVTNAQASMF TNLTFSGARY TGLGDMDAIA ILVTTPTGAV 

       310        320        330        340        350        360 
NTAVLKVWAC VEYRPNPNST LYEFARESPA NDEYALAAYR KIARDIPIAV ACKDNATFWE 

       370        380        390 
RVRSILKSGL NFASTIPGPV GVAATGIKGI IETIGSLWV 

« 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]"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).

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X15961 Genomic RNA. Translation: CAA34083.1.
AF174534 Genomic RNA. Translation: AAF97862.1.
PIRVCBBND. C34011.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1NOVX-ray3.50A/B/C1-355[»]
D/E/F356-399[»]
ProteinModelPortalP12871.
SMRP12871. Positions 19-355.
ModBaseSearch...
MobiDBSearch...

Protein family/group databases

MEROPSN01.001.
TCDB1.A.61.1.1. the insect nodavirus channel-forming chain f (gamma-peptide) family.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

InterProIPR000696. Peptidase_A6.
[Graphical view]
PfamPF01829. Peptidase_A6. 1 hit.
[Graphical view]
PRINTSPR00863. NODAVIRPTASE.
ProtoNetSearch...

Other

EvolutionaryTraceP12871.

Entry information

Entry nameCAPSD_NODAM
AccessionPrimary (citable) accession number: P12871
Secondary accession number(s): Q9IMM2
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: February 19, 2014
This is version 98 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