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Protein

Capsid protein

Gene

ORF4

Organism
Carnation mottle virus (CarMV)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Capsid protein self-assembles to form an icosahedral capsid with a T=3 symmetry, about 32-35 nm in diameter, and consisting of 180 capsid proteins. Also acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs (By similarity).By similarity

Cofactori

Ca2+By similarityNote: Binds Ca(2+). Ca2+ probably promotes virus assembly and stabilize the virus particle.By similarity

GO - Molecular functioni

Complete GO annotation...

Keywords - Ligandi

Calcium, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Capsid protein
Alternative name(s):
Coat protein
p38
Gene namesi
ORF Names:ORF4
OrganismiCarnation mottle virus (CarMV)
Taxonomic identifieri11986 [NCBI]
Taxonomic lineageiVirusesssRNA positive-strand viruses, no DNA stageTombusviridaeCarmovirus
Virus hostiBegonia [TaxID: 3681]
Dianthus barbatus [TaxID: 278075]
Dianthus caryophyllus (Carnation) (Clove pink) [TaxID: 3570]
Dianthus chinensis [TaxID: 118431]
Dianthus superbus [TaxID: 288950]
Malus domestica (Apple) (Pyrus malus) [TaxID: 3750]
Saponaria officinalis (Common soapwort) (Lychnis saponaria) [TaxID: 3572]

Subcellular locationi

GO - Cellular componenti

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 – 348348Capsid proteinPRO_0000222860Add
BLAST

Interactioni

Subunit structurei

Homodimer. Homomultimer.By similarity

Structurei

Secondary structure

1
348
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi84 – 9512Combined sources
Beta strandi98 – 1014Combined sources
Beta strandi103 – 1097Combined sources
Turni114 – 1163Combined sources
Helixi118 – 1247Combined sources
Beta strandi127 – 14115Combined sources
Beta strandi150 – 1578Combined sources
Helixi167 – 1715Combined sources
Beta strandi173 – 1808Combined sources
Beta strandi185 – 1895Combined sources
Helixi206 – 2094Combined sources
Beta strandi212 – 2198Combined sources
Beta strandi221 – 2255Combined sources
Beta strandi227 – 24216Combined sources
Beta strandi249 – 2513Combined sources
Helixi255 – 2573Combined sources
Beta strandi263 – 2686Combined sources
Beta strandi271 – 2766Combined sources
Beta strandi278 – 28710Combined sources
Beta strandi289 – 2946Combined sources
Beta strandi298 – 3014Combined sources
Beta strandi304 – 3118Combined sources
Turni312 – 3154Combined sources
Beta strandi316 – 32510Combined sources
Beta strandi328 – 3347Combined sources
Beta strandi342 – 3476Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1OPOX-ray3.20A/B/C1-348[»]
ProteinModelPortaliP04383.
SMRiP04383. Positions 81-348.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04383.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 8181R domain, disordered, interaction with RNAAdd
BLAST
Regioni82 – 239158S domain, virion shellAdd
BLAST
Regioni240 – 348109P domain, projectingAdd
BLAST

Sequence similaritiesi

Family and domain databases

Gene3Di2.60.120.20. 1 hit.
InterProiIPR000937. Capsid_prot_S-dom_vir.
IPR013669. Coat_prot_C_Carmovir.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF08462. Carmo_coat_C. 1 hit.
PF00729. Viral_coat. 1 hit.
[Graphical view]
PRINTSiPR00233. ICOSAHEDRAL.
PROSITEiPS00555. ICOSAH_VIR_COAT_S. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P04383-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MENKGEKIAM NPTVQTLAQK GDKLAVKLVT RGWASLSTNQ KRRAEMLAGY
60 70 80 90 100
TPAILAFTPR RPRMTNPPPR TSRNSPGQAG KSMTMSKTEL LSTVKGTTGV
110 120 130 140 150
IPSFEDWVVS PRNVAVFPQL SLLATNFNKY RITALTVKYS PACSFETNGR
160 170 180 190 200
VALGFNDDAS DTPPTTKVGF YDLGKHVETA AQTAKDLVIP VDGKTRFIRD
210 220 230 240 250
SASDDAKLVD FGRIVLSTYG FDKADTVVGE LFIQYTIVLS DPTKTAKISQ
260 270 280 290 300
ASNDKVSDGP TYVVPSVNGN ELQLRVVAAG KWCIIVRGTV EGGFTKPTLI
310 320 330 340
GPGISGDVDY ESARPIAVCE LVTQMEGQIL KITKTSAEQP LQWVVYRM
Length:348
Mass (Da):37,787
Last modified:March 20, 1987 - v1
Checksum:iE9EEA336C45B0D39
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02986 Genomic RNA. Translation: CAA26728.1.
PIRiA04209. VCVECV.
RefSeqiYP_009032648.1. NC_001265.2.

Genome annotation databases

GeneIDi19493256.
KEGGivg:19493256.

Cross-referencesi

Web resourcesi

Virus Particle ExploreR db

Icosahedral capsid structure

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02986 Genomic RNA. Translation: CAA26728.1.
PIRiA04209. VCVECV.
RefSeqiYP_009032648.1. NC_001265.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1OPOX-ray3.20A/B/C1-348[»]
ProteinModelPortaliP04383.
SMRiP04383. Positions 81-348.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi19493256.
KEGGivg:19493256.

Miscellaneous databases

EvolutionaryTraceiP04383.

Family and domain databases

Gene3Di2.60.120.20. 1 hit.
InterProiIPR000937. Capsid_prot_S-dom_vir.
IPR013669. Coat_prot_C_Carmovir.
IPR029053. Viral_coat.
[Graphical view]
PfamiPF08462. Carmo_coat_C. 1 hit.
PF00729. Viral_coat. 1 hit.
[Graphical view]
PRINTSiPR00233. ICOSAHEDRAL.
PROSITEiPS00555. ICOSAH_VIR_COAT_S. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Nucleotide sequence and genome organization of carnation mottle virus RNA."
    Guilley H., Carrington J.C., Balazs E., Jonard G., Richards K., Morris T.J.
    Nucleic Acids Res. 13:6663-6677(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS).

Entry informationi

Entry nameiCAPSD_CARMV
AccessioniPrimary (citable) accession number: P04383
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 20, 1987
Last sequence update: March 20, 1987
Last modified: April 1, 2015
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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.