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Protein

Capsid protein alpha

Gene

alpha

Organism
Pariacoto virus (PaV)
Status
Reviewed-Annotation score: Annotation score: 4 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. 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

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

Keywords - Ligandi

Calcium, 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]

Subcellular locationi

Peptide gamma :
  • Virion Curated

  • Note: located inside the capsid.Curated

GO - Cellular componenti

Complete GO annotation...

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

Structurei

Secondary structure

1401
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni20 – 22Combined sources3
Beta strandi46 – 48Combined sources3
Helixi54 – 64Combined sources11
Beta strandi68 – 71Combined sources4
Beta strandi83 – 98Combined sources16
Beta strandi100 – 108Combined sources9
Beta strandi114 – 121Combined sources8
Beta strandi129 – 134Combined sources6
Helixi138 – 142Combined sources5
Turni146 – 149Combined sources4
Turni151 – 153Combined sources3
Beta strandi155 – 170Combined sources16
Turni174 – 176Combined sources3
Beta strandi180 – 186Combined sources7
Beta strandi189 – 200Combined sources12
Beta strandi207 – 218Combined sources12
Helixi219 – 221Combined sources3
Beta strandi223 – 225Combined sources3
Beta strandi228 – 234Combined sources7
Helixi235 – 237Combined sources3
Beta strandi239 – 242Combined sources4
Beta strandi247 – 249Combined sources3
Beta strandi256 – 266Combined sources11
Beta strandi274 – 276Combined sources3
Helixi278 – 281Combined sources4
Beta strandi294 – 301Combined sources8
Beta strandi307 – 321Combined sources15
Helixi328 – 330Combined sources3
Helixi339 – 348Combined sources10
Helixi363 – 374Combined sources12
Beta strandi379 – 381Combined sources3

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...

Miscellaneous databases

EvolutionaryTraceiQ9J7Z0.

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase A6 family.Curated

Family and domain databases

Gene3Di1.20.5.280. 1 hit.
2.60.120.20. 1 hit.
InterProiIPR023348. Pariacoto_capsid_alpha_C.
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.

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.

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...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi956349.
KEGGivg:956349.

Miscellaneous databases

EvolutionaryTraceiQ9J7Z0.

Family and domain databases

Gene3Di1.20.5.280. 1 hit.
2.60.120.20. 1 hit.
InterProiIPR023348. Pariacoto_capsid_alpha_C.
IPR000696. Peptidase_A6.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF01829. Peptidase_A6. 1 hit.
[Graphical view]
PRINTSiPR00863. NODAVIRPTASE.
ProtoNetiSearch...

Entry informationi

Entry nameiCAPSD_PAV
AccessioniPrimary (citable) accession number: Q9J7Z0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 16, 2002
Last sequence update: October 1, 2000
Last modified: November 2, 2016
This is version 86 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.