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P12871

- CAPSD_NODAM

UniProt

P12871 - CAPSD_NODAM

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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

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.
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 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 – 671 By 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
Complete GO annotation...

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 Capsid protein beta : Virion Reviewed prediction
Chain Peptide gamma : Virion Reviewed prediction
Note: located inside the capsid Reviewed prediction.

GO - Cellular componenti

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

Keywords - Cellular componenti

Capsid protein, T=3 icosahedral capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 399399Capsid protein alpha
PRO_0000402389Add
BLAST
Chaini1 – 355355Capsid protein beta
PRO_0000039196Add
BLAST
Chaini356 – 39944Peptide gamma
PRO_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

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.

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.

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

Sequence conflict

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

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: July 9, 2014
This is version 101 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

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