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Protein

Capsid protein alpha

Gene

alpha

Organism
Flock house virus (FHV)
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, 240 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.
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 (Probable).Curated

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 sitei75By 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

Protein family/group databases

MEROPSiN01.001.

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
OrganismiFlock house virus (FHV)
Taxonomic identifieri12287 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageNodaviridaeAlphanodavirus
Virus hostiCostelytra zealandica [TaxID: 50579]
Galleria mellonella (Greater wax moth) [TaxID: 7137]
Hordeum vulgare (Barley) [TaxID: 4513]
Saccharomyces cerevisiae (Baker's yeast) [TaxID: 4932]

Subcellular locationi

Peptide gamma :
  • Virion Curated

  • Note: Located inside the capsid and probably externalized in early endosomes.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_00004023881 – 407Capsid protein alphaAdd BLAST407
ChainiPRO_00000391941 – 363Capsid protein betaAdd BLAST363
ChainiPRO_0000039195364 – 407Peptide gammaAdd BLAST44

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi69 ↔ 318

Post-translational modificationi

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

Keywords - PTMi

Disulfide bond

Structurei

Secondary structure

1407
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi61 – 71Combined sources11
Beta strandi76 – 78Combined sources3
Beta strandi90 – 105Combined sources16
Beta strandi109 – 115Combined sources7
Beta strandi121 – 129Combined sources9
Beta strandi139 – 144Combined sources6
Helixi148 – 152Combined sources5
Beta strandi161 – 177Combined sources17
Turni181 – 183Combined sources3
Beta strandi187 – 193Combined sources7
Beta strandi196 – 204Combined sources9
Beta strandi210 – 219Combined sources10
Helixi220 – 224Combined sources5
Beta strandi228 – 234Combined sources7
Helixi235 – 237Combined sources3
Beta strandi239 – 242Combined sources4
Beta strandi247 – 249Combined sources3
Beta strandi260 – 263Combined sources4
Helixi269 – 272Combined sources4
Beta strandi275 – 279Combined sources5
Turni283 – 285Combined sources3
Beta strandi296 – 302Combined sources7
Beta strandi309 – 323Combined sources15
Helixi329 – 332Combined sources4
Helixi341 – 353Combined sources13
Beta strandi356 – 358Combined sources3
Helixi360 – 362Combined sources3
Helixi367 – 379Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3LOBX-ray3.60A/B/C1-363[»]
D/E/F364-407[»]
4FSJX-ray3.50A/B/C1-363[»]
D/E/F364-407[»]
4FTBX-ray2.70A/B/C1-363[»]
D/E/F364-407[»]
4FTEX-ray3.50A/B/C1-407[»]
4FTSX-ray3.20A/B/C1-407[»]
ProteinModelPortaliP12870.
SMRiP12870.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12870.

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi35 – 49Poly-ArgAdd BLAST15

Sequence similaritiesi

Belongs to the peptidase A6 family.Curated

Family and domain databases

Gene3Di2.60.120.20. 1 hit.
4.10.180.10. 1 hit.
InterProiIPR027440. Capsid_prot_alpha-like_dom.
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.

P12870-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVNNNRPRRQ RAQRVVVTTT QTAPVPQQNV PRNGRRRRNR TRRNRRRVRG
60 70 80 90 100
MNMAALTRLS QPGLAFLKCA FAPPDFNTDP GKGIPDRFEG KVVSRKDVLN
110 120 130 140 150
QSISFTAGQD TFILIAPTPG VAYWSASVPA GTFPTSATTF NPVNYPGFTS
160 170 180 190 200
MFGTTSTSRS DQVSSFRYAS MNVGIYPTSN LMQFAGSITV WKCPVKLSTV
210 220 230 240 250
QFPVATDPAT SSLVHTLVGL DGVLAVGPDN FSESFIKGVF SQSACNEPDF
260 270 280 290 300
EFNDILEGIQ TLPPANVSLG STGQPFTMDS GAEATSGVVG WGNMDTIVIR
310 320 330 340 350
VSAPEGAVNS AILKAWSCIE YRPNPNAMLY QFGHDSPPLD EVALQEYRTV
360 370 380 390 400
ARSLPVAVIA AQNASMWERV KSIIKSSLAA ASNIPGPIGV AASGISGLSA

LFEGFGF
Length:407
Mass (Da):43,710
Last modified:October 1, 1989 - v1
Checksum:i5A66E01BAD2FEB0B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15959 Genomic RNA. Translation: CAA34081.1.
PIRiB34011. VCBBFH.
RefSeqiNP_689442.1. NC_004144.1.

Genome annotation databases

GeneIDi962115.
KEGGivg:962115.

Cross-referencesi

Web resourcesi

Virus Particle ExploreR db

Icosahedral capsid structure

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15959 Genomic RNA. Translation: CAA34081.1.
PIRiB34011. VCBBFH.
RefSeqiNP_689442.1. NC_004144.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3LOBX-ray3.60A/B/C1-363[»]
D/E/F364-407[»]
4FSJX-ray3.50A/B/C1-363[»]
D/E/F364-407[»]
4FTBX-ray2.70A/B/C1-363[»]
D/E/F364-407[»]
4FTEX-ray3.50A/B/C1-407[»]
4FTSX-ray3.20A/B/C1-407[»]
ProteinModelPortaliP12870.
SMRiP12870.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiN01.001.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi962115.
KEGGivg:962115.

Miscellaneous databases

EvolutionaryTraceiP12870.

Family and domain databases

Gene3Di2.60.120.20. 1 hit.
4.10.180.10. 1 hit.
InterProiIPR027440. Capsid_prot_alpha-like_dom.
IPR000696. Peptidase_A6.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF01829. Peptidase_A6. 1 hit.
[Graphical view]
PRINTSiPR00863. NODAVIRPTASE.
ProtoNetiSearch...

Entry informationi

Entry nameiCAPSD_FHV
AccessioniPrimary (citable) accession number: P12870
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: November 2, 2016
This is version 99 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.