Q9J7Z0 (CAPSD_PAV) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Pariacoto virus (PaV)

Taxonomic identifier

103782 [NCBI]

Taxonomic lineage

Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Nodaviridae › Alphanodavirus

Virus host

Spodoptera eridania (Southern armyworm) [TaxID: 37547]

Protein attributes

Sequence length	401 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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. 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 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.
Mass spectrometry	Molecular mass is 4246 Da from positions 362 - 401. Determined by MALDI. Ref.1

Ontologies

Keywords
Biological process	Viral penetration into host cytoplasm Viral penetration via permeabilization of host organellar membrane Virus entry into host cell
Cellular component	Virion
Ligand	Calcium Metal-binding
Molecular function	Aspartyl protease Capsid protein Hydrolase Protease T=3 icosahedral capsid protein
PTM	Disulfide bond
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	proteolysis Inferred from electronic annotation. Source: UniProtKB-KW viral entry into host cell Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	T=3 icosahedral viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	aspartic-type endopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 401

401

Capsid protein alpha

PRO_0000402390

Chain

1 – 361

361

Capsid protein beta

PRO_0000039198

Chain

362 – 401

40

Peptide gamma

PRO_0000039199

Sites

Active site

68

1

By similarity

Metal binding

249

1

Calcium

Metal binding

251

1

Calcium

Amino acid modifications

Disulfide bond

62 ↔ 316

By similarity

Secondary structure

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401

Helix Strand Turn

Details...

Turn

20 – 22

3

Beta strand

46 – 48

3

Helix

54 – 64

11

Beta strand

68 – 71

4

Beta strand

83 – 98

16

Beta strand

100 – 108

9

Beta strand

114 – 121

8

Beta strand

129 – 134

6

Helix

138 – 142

5

Turn

146 – 149

4

Turn

151 – 153

3

Beta strand

155 – 170

16

Turn

174 – 176

3

Beta strand

180 – 186

7

Beta strand

189 – 200

12

Beta strand

207 – 218

12

Helix

219 – 221

3

Beta strand

223 – 225

3

Beta strand

228 – 234

7

Helix

235 – 237

3

Beta strand

239 – 242

4

Beta strand

247 – 249

3

Beta strand

256 – 266

11

Beta strand

274 – 276

3

Helix

278 – 281

4

Beta strand

294 – 301

8

Beta strand

307 – 321

15

Helix

328 – 330

3

Helix

339 – 348

10

Helix

363 – 374

12

Sequences

	Sequence		Length	Mass (Da)
	Q9J7Z0 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: 1E518977DE7A2C90	FASTA	401	43,326
	10 20 30 40 50 60 MVSRTKNRRN KARKVVSRST ALVPMAPASQ RTGPAPRKPR KRNQALVRNP RLTDAGLAFL 70 80 90 100 110 120 KCAFAAPDFS VDPGKGIPDN FHGRTLAIKD CNTTSVVFTP NTDTYIVVAP VPGFAYFRAE 130 140 150 160 170 180 VAVGAQPTTF VGVPYPTYAT NFGAGSQNGL PAVNNYSKFR YASMACGLYP TSNMMQFSGS 190 200 210 220 230 240 VQVWRVDLNL SEAVNPAVTA ITPAPGVFAN FVDKRINGLR GIRPLAPRDN YSGNFIDGAY 250 260 270 280 290 300 TFAFDKSTDF EWCDFVRSLE FSESNVLGAA TAMKLLAPGG GTDTTLTGLG NVNTLVYKIS 310 320 330 340 350 360 TPTGAVNTAI LRTWNCIELQ PYTDSALFQF SGVSPPFDPL ALECYHNLKM RFPVAVSSRE 370 380 390 400 NSKFWEGVLR VLNQISGTLS VIPGPVGTIS AGVHQLTGMY M

References

[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.

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF171943 Genomic RNA. Translation: AAF71693.1.

RefSeq

NP_620111.1. NC_003692.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1F8V	X-ray	3.00	A/B/C	7-361	[»]
			D/E/F	362-401	[»]

ProteinModelPortal

Q9J7Z0.

SMR

Q9J7Z0. Positions 7-361.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

1.20.5.280. 1 hit.

InterPro

IPR023348. Pariacoto_capsid_alpha_C.
IPR000696. Peptidase_A6.
[Graphical view]

Pfam

PF01829. Peptidase_A6. 1 hit.
[Graphical view]

PRINTS

PR00863. NODAVIRPTASE.

ProtoNet

Search...

Other

EvolutionaryTrace

Q9J7Z0.

Entry information

Entry name

CAPSD_PAV

Accession

Primary (citable) accession number: Q9J7Z0

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 16, 2002
Last sequence update:	October 1, 2000
Last modified:	April 3, 2013
This is version 70 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program