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Protein

Capsid protein alpha

Gene

alpha

Organism
Nodamura virus (strain Mag115) (NoV)
Status
Reviewed-Annotation score: 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).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 sitei67By similarity1

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

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 virusesssRNA positive-strand viruses, no DNA stageNodaviridaeAlphanodavirus
Virus hostiAedes [TaxID: 7158]
Lepidoptera (butterflies and moths) [TaxID: 7088]
Sus scrofa (Pig) [TaxID: 9823]
Proteomesi
  • UP000008594 Componenti: Genome

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_00004023891 – 399Capsid protein alphaAdd BLAST399
ChainiPRO_00000391961 – 355Capsid protein betaAdd BLAST355
ChainiPRO_0000039197356 – 399Peptide gammaAdd BLAST44

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
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

1399
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi11 – 15Combined sources5
Helixi53 – 63Combined sources11
Helixi65 – 67Combined sources3
Beta strandi68 – 70Combined sources3
Beta strandi82 – 97Combined sources16
Beta strandi101 – 107Combined sources7
Beta strandi113 – 121Combined sources9
Beta strandi131 – 135Combined sources5
Helixi139 – 142Combined sources4
Beta strandi152 – 160Combined sources9
Beta strandi163 – 168Combined sources6
Turni172 – 174Combined sources3
Beta strandi178 – 184Combined sources7
Beta strandi188 – 197Combined sources10
Beta strandi199 – 201Combined sources3
Beta strandi203 – 213Combined sources11
Helixi215 – 219Combined sources5
Beta strandi226 – 229Combined sources4
Beta strandi234 – 237Combined sources4
Beta strandi242 – 244Combined sources3
Beta strandi255 – 258Combined sources4
Turni264 – 268Combined sources5
Beta strandi276 – 278Combined sources3
Beta strandi288 – 295Combined sources8
Beta strandi301 – 315Combined sources15
Beta strandi319 – 321Combined sources3
Helixi333 – 345Combined sources13
Helixi358 – 369Combined sources12
Helixi370 – 372Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NOVX-ray3.50A/B/C1-355[»]
D/E/F356-399[»]
ProteinModelPortaliP12871.
SMRiP12871.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12871.

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi7 – 10Poly-Arg4
Compositional biasi29 – 38Poly-Arg10

Sequence similaritiesi

Belongs to the peptidase A6 family.Curated

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

« Hide

        10         20         30         40         50
MVSKAARRRR AAPRQQQRQQ SNRASNQPRR RRARRTRRQQ RMAATNNMLK
60 70 80 90 100
MSAPGLDFLK CAFASPDFST DPGKGIPDKF QGLVLPKKHC LTQSITFTPG
110 120 130 140 150
KQTMLLVAPI PGIACLKAEA NVGASFSGVP LASVEFPGFD QLFGTSATDT
160 170 180 190 200
AANVTAFRYA SMAAGVYPTS NLMQFAGSIQ VYKIPLKQVL NSYSQTVATV
210 220 230 240 250
PPTNLAQNTI AIDGLEALDA LPNNNYSGSF IEGCYSQSVC NEPEFEFHPI
260 270 280 290 300
MEGYASVPPA NVTNAQASMF TNLTFSGARY TGLGDMDAIA ILVTTPTGAV
310 320 330 340 350
NTAVLKVWAC VEYRPNPNST LYEFARESPA NDEYALAAYR KIARDIPIAV
360 370 380 390
ACKDNATFWE RVRSILKSGL NFASTIPGPV GVAATGIKGI IETIGSLWV
Length:399
Mass (Da):43,067
Last modified:October 1, 1989 - v1
Checksum:iA026158C6548060B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti279R → A in AAF97862 (Ref. 2) Curated1
Sequence conflicti393T → A in AAF97862 (Ref. 2) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
Links Updated
X15961 Genomic RNA. Translation: CAA34083.1.
AF174534 Genomic RNA. Translation: AAF97862.1.
PIRiC34011. VCBBND.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NOVX-ray3.50A/B/C1-355[»]
D/E/F356-399[»]
ProteinModelPortaliP12871.
SMRiP12871.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiN01.001.
TCDBi1.A.61.1.1. the insect nodavirus channel-forming chain f (gamma-peptide) family.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP12871.

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.
ProtoNetiSearch...

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: November 2, 2016
This is version 111 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

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.