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Protein

Capsid protein alpha

Gene

alpha

Organism
Pariacoto virus (PaV)
Status
Reviewed-Annotation score: -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. In addition, 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 (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)DescriptionActionsGraphical viewLength
Active sitei68By similarity1
Metal bindingi249Calcium1
Metal bindingi251Calcium1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionAspartyl protease, Hydrolase, Protease
Biological processViral penetration into host cytoplasm, Viral penetration via permeabilization of host membrane, Virus entry into host cell
LigandCalcium, Metal-binding

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
OrganismiPariacoto virus (PaV)
Taxonomic identifieri103782 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageNodaviridaeAlphanodavirus
Virus hostiSpodoptera eridania (Southern armyworm) [TaxID: 37547]
Proteomesi
  • UP000204174 Componenti: Genome

Subcellular locationi

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

GO - Cellular componenti

Keywords - Cellular componenti

Capsid protein, T=3 icosahedral capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004023901 – 401Capsid protein alphaAdd BLAST401
ChainiPRO_00000391981 – 361Capsid protein betaAdd BLAST361
ChainiPRO_0000039199362 – 401Peptide gammaAdd BLAST40

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi62 ↔ 316By similarity

Post-translational modificationi

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

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiQ9J7Z0

Structurei

Secondary structure

1401
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ9J7Z0
SMRiQ9J7Z0
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9J7Z0

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase A6 family.Curated

Family and domain databases

Gene3Di2.60.120.20, 1 hit
InterProiView protein in InterPro
IPR000696 Peptidase_A6
IPR029053 Viral_coat
PfamiView protein in Pfam
PF01829 Peptidase_A6, 1 hit
PRINTSiPR00863 NODAVIRPTASE

Sequencei

Sequence statusi: Complete.

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

Q9J7Z0-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MVSRTKNRRN KARKVVSRST ALVPMAPASQ RTGPAPRKPR KRNQALVRNP
60 70 80 90 100
RLTDAGLAFL KCAFAAPDFS VDPGKGIPDN FHGRTLAIKD CNTTSVVFTP
110 120 130 140 150
NTDTYIVVAP VPGFAYFRAE VAVGAQPTTF VGVPYPTYAT NFGAGSQNGL
160 170 180 190 200
PAVNNYSKFR YASMACGLYP TSNMMQFSGS VQVWRVDLNL SEAVNPAVTA
210 220 230 240 250
ITPAPGVFAN FVDKRINGLR GIRPLAPRDN YSGNFIDGAY TFAFDKSTDF
260 270 280 290 300
EWCDFVRSLE FSESNVLGAA TAMKLLAPGG GTDTTLTGLG NVNTLVYKIS
310 320 330 340 350
TPTGAVNTAI LRTWNCIELQ PYTDSALFQF SGVSPPFDPL ALECYHNLKM
360 370 380 390 400
RFPVAVSSRE NSKFWEGVLR VLNQISGTLS VIPGPVGTIS AGVHQLTGMY

M
Length:401
Mass (Da):43,326
Last modified:October 1, 2000 - v1
Checksum:i1E518977DE7A2C90
GO

Mass spectrometryi

Molecular mass is 4246 Da from positions 362 - 401. Determined by MALDI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF171943 Genomic RNA Translation: AAF71693.1
RefSeqiNP_620111.1, NC_003692.1

Genome annotation databases

GeneIDi956349
KEGGivg:956349

Similar proteinsi

Cross-referencesi

Web resourcesi

Virus Particle ExploreR db

Icosahedral capsid structure

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF171943 Genomic RNA Translation: AAF71693.1
RefSeqiNP_620111.1, NC_003692.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1F8VX-ray3.00A/B/C7-361[»]
D/E/F362-401[»]
ProteinModelPortaliQ9J7Z0
SMRiQ9J7Z0
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ9J7Z0

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi956349
KEGGivg:956349

Miscellaneous databases

EvolutionaryTraceiQ9J7Z0

Family and domain databases

Gene3Di2.60.120.20, 1 hit
InterProiView protein in InterPro
IPR000696 Peptidase_A6
IPR029053 Viral_coat
PfamiView protein in Pfam
PF01829 Peptidase_A6, 1 hit
PRINTSiPR00863 NODAVIRPTASE
ProtoNetiSearch...

Entry informationi

Entry nameiCAPSD_PAV
AccessioniPrimary (citable) accession number: Q9J7Z0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 16, 2002
Last sequence update: October 1, 2000
Last modified: May 23, 2018
This is version 91 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Peptidase families
    Classification of peptidase families and list of entries
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Main funding by: National Institutes of Health

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