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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 Ca2+. 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 virusesssRNA 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)DescriptionActionsGraphical viewLength
ChainiPRO_00002228601 – 348Capsid proteinAdd BLAST348

Interactioni

Subunit structurei

Homodimer. Homomultimer.By similarity

Structurei

Secondary structure

1348
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi84 – 95Combined sources12
Beta strandi98 – 101Combined sources4
Beta strandi103 – 109Combined sources7
Turni114 – 116Combined sources3
Helixi118 – 124Combined sources7
Beta strandi127 – 141Combined sources15
Beta strandi150 – 157Combined sources8
Helixi167 – 171Combined sources5
Beta strandi173 – 180Combined sources8
Beta strandi185 – 189Combined sources5
Helixi206 – 209Combined sources4
Beta strandi212 – 219Combined sources8
Beta strandi221 – 225Combined sources5
Beta strandi227 – 242Combined sources16
Beta strandi249 – 251Combined sources3
Helixi255 – 257Combined sources3
Beta strandi263 – 268Combined sources6
Beta strandi271 – 276Combined sources6
Beta strandi278 – 287Combined sources10
Beta strandi289 – 294Combined sources6
Beta strandi298 – 301Combined sources4
Beta strandi304 – 311Combined sources8
Turni312 – 315Combined sources4
Beta strandi316 – 325Combined sources10
Beta strandi328 – 334Combined sources7
Beta strandi342 – 347Combined sources6

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP04383.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 81R domain, disordered, interaction with RNAAdd BLAST81
Regioni82 – 239S domain, virion shellAdd BLAST158
Regioni240 – 348P domain, projectingAdd BLAST109

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1OPOX-ray3.20A/B/C1-348[»]
ProteinModelPortaliP04383.
SMRiP04383.
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...

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: November 2, 2016
This is version 81 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

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.