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P12870

- CAPSD_FHV

UniProt

P12870 - CAPSD_FHV

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Protein

Capsid protein alpha

Gene

alpha

Organism
Flock house virus (FHV)
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, 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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei75 – 751By 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

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 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

Chain Peptide gamma : Virion Curated
Note: Located inside the capsid and probably externalized in early endosomes.Curated

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 – 407407Capsid protein alphaPRO_0000402388Add
BLAST
Chaini1 – 363363Capsid protein betaPRO_0000039194Add
BLAST
Chaini364 – 40744Peptide gammaPRO_0000039195Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
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

1
407
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi61 – 7111
Beta strandi76 – 783
Beta strandi90 – 10516
Beta strandi109 – 1157
Beta strandi121 – 1299
Beta strandi139 – 1446
Helixi148 – 1525
Beta strandi161 – 17717
Turni181 – 1833
Beta strandi187 – 1937
Beta strandi196 – 2049
Beta strandi210 – 21910
Helixi220 – 2245
Beta strandi228 – 2347
Helixi235 – 2373
Beta strandi239 – 2424
Beta strandi247 – 2493
Beta strandi260 – 2634
Helixi269 – 2724
Beta strandi275 – 2795
Turni283 – 2853
Beta strandi296 – 3027
Beta strandi309 – 32315
Helixi329 – 3324
Helixi341 – 35313
Beta strandi356 – 3583
Helixi360 – 3623
Helixi367 – 37913

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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. Positions 19-363.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12870.

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi35 – 4915Poly-ArgAdd
BLAST

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:
EMBL
GenBank
DDBJ
Links Updated
X15959 Genomic RNA. Translation: CAA34081.1.
PIRiB34011. VCBBFH.
RefSeqiNP_689442.1. NC_004144.1.

Genome annotation databases

GeneIDi962115.

Cross-referencesi

Web resourcesi

Virus Particle ExploreR db

Icosahedral capsid structure

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X15959 Genomic RNA. Translation: CAA34081.1 .
PIRi B34011. VCBBFH.
RefSeqi NP_689442.1. NC_004144.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3LOB X-ray 3.60 A/B/C 1-363 [» ]
D/E/F 364-407 [» ]
4FSJ X-ray 3.50 A/B/C 1-363 [» ]
D/E/F 364-407 [» ]
4FTB X-ray 2.70 A/B/C 1-363 [» ]
D/E/F 364-407 [» ]
4FTE X-ray 3.50 A/B/C 1-407 [» ]
4FTS X-ray 3.20 A/B/C 1-407 [» ]
ProteinModelPortali P12870.
SMRi P12870. Positions 19-363.
ModBasei Search...
MobiDBi Search...

Protein family/group databases

MEROPSi N01.001.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 962115.

Miscellaneous databases

EvolutionaryTracei P12870.

Family and domain databases

Gene3Di 2.60.120.20. 1 hit.
4.10.180.10. 1 hit.
InterProi IPR027440. Capsid_prot_alpha-like_dom.
IPR000696. Peptidase_A6.
IPR029053. Viral_coat.
[Graphical view ]
Pfami PF01829. Peptidase_A6. 1 hit.
[Graphical view ]
PRINTSi PR00863. NODAVIRPTASE.
ProtoNeti Search...

Publicationsi

  1. "Nucleotide sequences of three Nodavirus RNA2's: the messengers for their coat protein precursors."
    Dasgupta R., Sgro J.-Y.
    Nucleic Acids Res. 17:7525-7526(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. "Structural homology among four nodaviruses as deduced by sequencing and X-ray crystallography."
    Kaesberg P., Dasgupta R., Sgro J.-Y., Wery J.-P., Selling B.H., Hosur M.V., Johnson J.E.
    J. Mol. Biol. 214:423-435(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: SIMILARITY TO OTHER NODAVIRUSES.
  3. "Specific encapsidation of nodavirus RNAs is mediated through the C terminus of capsid precursor protein alpha."
    Schneemann A., Marshall D.
    J. Virol. 72:8738-8746(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF PEPTIDE GAMMA.
  4. "Low endocytic pH and capsid protein autocleavage are critical components of Flock House virus cell entry."
    Odegard A.L., Kwan M.H., Walukiewicz H.E., Banerjee M., Schneemann A., Johnson J.E.
    J. Virol. 83:8628-8637(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION OF PEPTIDE GAMMA, PROTEOLYTIC PROCESSING OF POLYPROTEIN.
  5. "Ordered duplex RNA controls capsid architecture in an icosahedral animal virus."
    Fisher A.J., Johnson J.E.
    Nature 361:176-179(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS).
  6. "Structure and function of a genetically engineered mimic of a nonenveloped virus entry intermediate."
    Banerjee M., Speir J.A., Kwan M.H., Huang R., Aryanpur P.P., Bothner B., Johnson J.E.
    J. Virol. 84:4737-4746(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.6 ANGSTROMS), FUNCTION.

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: October 1, 2014
This is version 91 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