P04383 (CAPSD_CARMV) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Capsid protein

Alternative name(s):
Coat protein
p38

Gene names

ORF Names:

ORF4

Organism

Carnation mottle virus (CarMV)

Taxonomic identifier

11986 [NCBI]

Taxonomic lineage

Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Tombusviridae › Carmovirus

Virus host

Begonia [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]

Protein attributes

Sequence length	348 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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.
Cofactor	Binds calcium ions. Calcium ions probably promote virus assembly and stabilize the virus particle By similarity.
Subunit structure	Homodimer By similarity. Homomultimer By similarity.
Subcellular location	Virion By similarity.
Sequence similarities	Belongs to the icosahedral plant coat protein family.

Ontologies

Keywords
Cellular component	Virion
Ligand	Calcium RNA-binding
Molecular function	Capsid protein T=3 icosahedral capsid protein
Technical term	3D-structure
Gene Ontology (GO)
Cellular_component	T=3 icosahedral viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW structural molecule activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 348

348

Capsid protein

PRO_0000222860

Regions

Region

1 – 81

81

R domain, disordered, interaction with RNA

Region

82 – 239

158

S domain, virion shell

Region

240 – 348

109

P domain, projecting

Secondary structure

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348

Helix Strand Turn

Details...

Beta strand

84 – 95

12

Beta strand

98 – 101

4

Beta strand

103 – 109

7

Turn

114 – 116

3

Helix

118 – 124

7

Beta strand

127 – 141

15

Beta strand

150 – 157

8

Helix

167 – 171

5

Beta strand

173 – 180

8

Beta strand

185 – 189

5

Helix

206 – 209

4

Beta strand

212 – 219

8

Beta strand

221 – 225

5

Beta strand

227 – 242

16

Beta strand

249 – 251

3

Helix

255 – 257

3

Beta strand

263 – 268

6

Beta strand

271 – 276

6

Beta strand

278 – 287

10

Beta strand

289 – 294

6

Beta strand

298 – 301

4

Beta strand

304 – 311

8

Turn

312 – 315

4

Beta strand

316 – 325

10

Beta strand

328 – 334

7

Beta strand

342 – 347

6

Sequences

	Sequence		Length	Mass (Da)
	P04383 [UniParc]. Last modified March 20, 1987. Version 1. Checksum: E9EEA336C45B0D39	FASTA	348	37,787
	10 20 30 40 50 60 MENKGEKIAM NPTVQTLAQK GDKLAVKLVT RGWASLSTNQ KRRAEMLAGY TPAILAFTPR 70 80 90 100 110 120 RPRMTNPPPR TSRNSPGQAG KSMTMSKTEL LSTVKGTTGV IPSFEDWVVS PRNVAVFPQL 130 140 150 160 170 180 SLLATNFNKY RITALTVKYS PACSFETNGR VALGFNDDAS DTPPTTKVGF YDLGKHVETA 190 200 210 220 230 240 AQTAKDLVIP VDGKTRFIRD SASDDAKLVD FGRIVLSTYG FDKADTVVGE LFIQYTIVLS 250 260 270 280 290 300 DPTKTAKISQ ASNDKVSDGP TYVVPSVNGN ELQLRVVAAG KWCIIVRGTV EGGFTKPTLI 310 320 330 340 GPGISGDVDY ESARPIAVCE LVTQMEGQIL KITKTSAEQP LQWVVYRM

References

[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]	"The atomic structure of Carnation mottle virus capsid protein." Morgunova E.Y., Dauter Z., Stuart D.I., Stel'Mashchuk V.Y., Mikhailov A.M., Wilson K.S., Vainshtein B.K. FEBS Lett. 338:267-271(1994) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS).

Web resources

Virus Particle ExploreR db

Icosahedral capsid structure

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X02986 Genomic RNA. Translation: CAA26728.1.

PIR

VCVECV. A04209.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1OPO	X-ray	3.20	A/B/C	1-348	[»]

ProteinModelPortal

P04383.

SMR

P04383. Positions 81-348.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR000937. Capsid_prot_S-dom_vir.
IPR013669. Coat_prot_C_Carmovir.
[Graphical view]

Pfam

PF08462. Carmo_coat_C. 1 hit.
PF00729. Viral_coat. 1 hit.
[Graphical view]

PRINTS

PR00233. ICOSAHEDRAL.

PROSITE

PS00555. ICOSAH_VIR_COAT_S. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P04383.

Entry information

Entry name

CAPSD_CARMV

Accession

Primary (citable) accession number: P04383

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 20, 1987
Last sequence update:	March 20, 1987
Last modified:	April 3, 2013
This is version 70 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program