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Q9J7Z0

- CAPSD_PAV

UniProt

Q9J7Z0 - CAPSD_PAV

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Protein
Capsid protein alpha
Gene
alpha
Organism
Pariacoto virus (PaV)
Status
Reviewed - 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.
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 sitei68 – 681 By similarity
Metal bindingi249 – 2491Calcium
Metal bindingi251 – 2511Calcium

GO - Molecular functioni

  1. aspartic-type endopeptidase activity Source: UniProtKB-KW
  2. metal ion binding 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

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 positive-strand viruses, no DNA stageNodaviridaeAlphanodavirus
Virus hostiSpodoptera eridania (Southern armyworm) [TaxID: 37547]

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 – 401401Capsid protein alpha
PRO_0000402390Add
BLAST
Chaini1 – 361361Capsid protein beta
PRO_0000039198Add
BLAST
Chaini362 – 40140Peptide gamma
PRO_0000039199Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi62 ↔ 316 By 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

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni20 – 223
Beta strandi46 – 483
Helixi54 – 6411
Beta strandi68 – 714
Beta strandi83 – 9816
Beta strandi100 – 1089
Beta strandi114 – 1218
Beta strandi129 – 1346
Helixi138 – 1425
Turni146 – 1494
Turni151 – 1533
Beta strandi155 – 17016
Turni174 – 1763
Beta strandi180 – 1867
Beta strandi189 – 20012
Beta strandi207 – 21812
Helixi219 – 2213
Beta strandi223 – 2253
Beta strandi228 – 2347
Helixi235 – 2373
Beta strandi239 – 2424
Beta strandi247 – 2493
Beta strandi256 – 26611
Beta strandi274 – 2763
Helixi278 – 2814
Beta strandi294 – 3018
Beta strandi307 – 32115
Helixi328 – 3303
Helixi339 – 34810
Helixi363 – 37412

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1F8VX-ray3.00A/B/C7-361[»]
D/E/F362-401[»]
ProteinModelPortaliQ9J7Z0.
SMRiQ9J7Z0. Positions 7-361.

Miscellaneous databases

EvolutionaryTraceiQ9J7Z0.

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase A6 family.

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

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MVSRTKNRRN KARKVVSRST ALVPMAPASQ RTGPAPRKPR KRNQALVRNP    50
RLTDAGLAFL KCAFAAPDFS VDPGKGIPDN FHGRTLAIKD CNTTSVVFTP 100
NTDTYIVVAP VPGFAYFRAE VAVGAQPTTF VGVPYPTYAT NFGAGSQNGL 150
PAVNNYSKFR YASMACGLYP TSNMMQFSGS VQVWRVDLNL SEAVNPAVTA 200
ITPAPGVFAN FVDKRINGLR GIRPLAPRDN YSGNFIDGAY TFAFDKSTDF 250
EWCDFVRSLE FSESNVLGAA TAMKLLAPGG GTDTTLTGLG NVNTLVYKIS 300
TPTGAVNTAI LRTWNCIELQ PYTDSALFQF SGVSPPFDPL ALECYHNLKM 350
RFPVAVSSRE NSKFWEGVLR VLNQISGTLS VIPGPVGTIS AGVHQLTGMY 400
M 401
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:
EMBL
GenBank
DDBJ
Links Updated
AF171943 Genomic RNA. Translation: AAF71693.1.
RefSeqiNP_620111.1. NC_003692.1.

Genome annotation databases

GeneIDi956349.

Cross-referencesi

Web resourcesi

Virus Particle ExploreR db

Icosahedral capsid structure

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF171943 Genomic RNA. Translation: AAF71693.1 .
RefSeqi NP_620111.1. NC_003692.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1F8V X-ray 3.00 A/B/C 7-361 [» ]
D/E/F 362-401 [» ]
ProteinModelPortali Q9J7Z0.
SMRi Q9J7Z0. Positions 7-361.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 956349.

Miscellaneous databases

EvolutionaryTracei Q9J7Z0.

Family and domain databases

Gene3Di 1.20.5.280. 1 hit.
2.60.120.20. 1 hit.
InterProi IPR023348. Pariacoto_capsid_alpha_C.
IPR000696. Peptidase_A6.
IPR029053. Viral_coat.
[Graphical view ]
Pfami PF01829. Peptidase_A6. 1 hit.
[Graphical view ]
PRINTSi PR00863. NODAVIRPTASE.
ProtoNeti Search...

Publicationsi

  1. "Characterization and construction of functional cDNA clones of Pariacoto virus, the first Alphanodavirus isolated outside Australasia."
    Johnson K.N., Zeddam J.-L., Ball L.A.
    J. Virol. 74:5123-5132(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA], MASS SPECTROMETRY.
  2. "The structure of pariacoto virus reveals a dodecahedral cage of duplex RNA."
    Tang L., Johnson K.N., Ball L.A., Lin T., Yeager M., Johnson J.E.
    Nat. Struct. Biol. 8:77-83(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 7-401.

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: July 9, 2014
This is version 76 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

External Data

Dasty 3

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