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Protein

Capsid protein

Gene
N/A
Organism
Escherichia phage MS2 (Bacteriophage MS2)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Capsid protein self-assembles to form an icosahedral capsid with a T=3 symmetry, about 26 nm in diameter, and consisting of 89 capsid proteins dimers (178 capsid proteins) (PubMed:8254664, PubMed:18662904). Involved in viral genome encapsidation through the interaction between a capsid protein dimer and the multiple packaging signals present in the RNA genome (PubMed:9469847, PubMed:26608810, PubMed:7523953). The capsid contains also 1 copy of the A2 maturation protein (PubMed:8254664).1 Publication5 Publications
Acts as a translational repressor of viral replicase synthesis late in infection. This latter function is the result of capsid protein interaction with an RNA hairpin which contains the replicase ribosome-binding site.3 Publications

GO - Molecular functioni

  • RNA binding Source: UniProtKB
  • structural molecule activity Source: InterPro

GO - Biological processi

Keywordsi

Molecular functionRNA-binding
Biological processTranslation regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Capsid protein
Short name:
CP
Alternative name(s):
Coat protein
OrganismiEscherichia phage MS2 (Bacteriophage MS2)
Taxonomic identifieri329852 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageLeviviridaeLevivirus
Virus hostiEscherichia coli [TaxID: 562]
Proteomesi
  • UP000002127 Componenti: Genome

Subcellular locationi

  • Virion 1 Publication

  • Note: The shell is composed of 178 copies of the capsid protein and 1 copy of the maturation protein.1 Publication1 Publication

GO - Cellular componenti

  • T=3 icosahedral viral capsid Source: UniProtKB

Keywords - Cellular componenti

Capsid protein, T=3 icosahedral capsid protein, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi46T → A: Loss of repression of replicase translation. 80% loss of binding to the operator RNA in vivo. 2 Publications1
Mutagenesisi60T → S: Loss of repression of replicase. 20% loss of binding to the operator RNA in vivo. 2 Publications1
Mutagenesisi77E → A: No effect on the organization of the T=3 capsid, but with a loss of thermal stability. No effect on infectivity. 1 Publication1
Mutagenesisi79P → A: No effect on the organization of the T=3 capsid, but with a loss of thermal stability. Complete loss of infectivity. 1 Publication1
Mutagenesisi83W → R: Complete loss of viral assembly. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by hostBy similarity
ChainiPRO_00001648432 – 130Capsid proteinAdd BLAST129

Interactioni

Subunit structurei

Homodimer (PubMed:8254664, PubMed:7788292, PubMed:19521994). The capsid proteins form dimers that assemble by group of 5. Twelve such pentamers are linked together with free dimers (PubMed:8254664). The homodimers binds to the viral RNA via an operator hairpin, but also to many other RNA sequences in the viral genome; this interaction probably shifts the virus from the replicative to the assembly phase and ensures specific encapsidation of the viral genome (PubMed:12948491).1 Publication3 Publications

Protein-protein interaction databases

DIPiDIP-37669N.

Structurei

Secondary structure

1130
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 11Combined sources4
Beta strandi13 – 17Combined sources5
Beta strandi19 – 27Combined sources9
Beta strandi30 – 34Combined sources5
Beta strandi38 – 40Combined sources3
Beta strandi44 – 53Combined sources10
Beta strandi56 – 65Combined sources10
Beta strandi70 – 75Combined sources6
Beta strandi79 – 83Combined sources5
Beta strandi85 – 94Combined sources10
Beta strandi95 – 97Combined sources3
Helixi99 – 112Combined sources14
Helixi118 – 125Combined sources8
Beta strandi126 – 129Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1AQ3X-ray2.80A/B/C2-130[»]
1AQ4X-ray3.00A/B/C2-130[»]
1BMSX-ray2.70A/B/C2-130[»]
1MSCX-ray2.00A2-130[»]
1MSTX-ray2.60A/B/C2-130[»]
1MVAX-ray3.00A/B/C2-130[»]
1MVBX-ray3.00A/B/C2-130[»]
1U1YX-ray2.85A/B/C2-130[»]
1ZDHX-ray2.70A/B/C2-130[»]
1ZDIX-ray2.70A/B/C2-130[»]
1ZDJX-ray2.90A/B/C2-130[»]
1ZDKX-ray2.86A/B/C2-130[»]
1ZSEX-ray3.00A/B/C2-130[»]
2B2DX-ray2.90A/B/C2-130[»]
2B2EX-ray3.15A/B/C2-130[»]
2B2GX-ray3.02A/B/C2-130[»]
2BNYX-ray3.00A/B/C2-130[»]
2BQ5X-ray2.91A/B/C2-130[»]
2BS0X-ray2.45A/B/C2-130[»]
2BS1X-ray2.80A/B/C2-130[»]
2BU1X-ray2.20A/B/C2-130[»]
2C4QX-ray2.38A/B/C2-130[»]
2C4YX-ray2.68A/B/C2-130[»]
2C4ZX-ray2.60A/B/C2-130[»]
2C50X-ray2.65A/B/C2-130[»]
2C51X-ray2.80A/B/C2-130[»]
2IZ8X-ray3.30A/B/C2-130[»]
2IZ9X-ray2.85A/B/C2-130[»]
2IZMX-ray2.70A/B/C2-130[»]
2IZNX-ray2.56A/B/C2-130[»]
2MS2X-ray2.80A/B/C2-130[»]
2VTUX-ray3.50J/L2-130[»]
2WBHX-ray4.70A/B/C2-130[»]
4BP7electron microscopy39.00A0/A1/A2/A3/A4/A5/A6/A7/A8/A9/AA/AB/AC/AD/AE/AF/AG/AH/AI/AJ/AK/AL/AM/AN/AO/AP/AQ/AR/AS/AT/AU/AV/AW/AX/AY/AZ/Aa/Ab/Ac/Ad/Ae/Af/Ag/Ah/Ai/Aj/Ak/Al/Am/An/Ao/Ap/Aq/Ar/As/At/Au/Av/Aw/Ax/B0/B1/B2/B3/B4/B5/B6/B7/B8/B9/BA2-130[»]
4ZORX-ray2.20A/B/C/D/E2-130[»]
5MSFX-ray2.80A/B/C2-130[»]
5TC1electron microscopy3.60A/B/C/D/E/F/G/H1-130[»]
6MSFX-ray2.80A/B/C2-130[»]
7MSFX-ray2.80A/B/C2-130[»]
ProteinModelPortaliP03612.
SMRiP03612.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03612.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni32 – 105Viral RNA-binding1 PublicationAdd BLAST74

Sequence similaritiesi

Belongs to the Levivirus capsid protein family.Curated

Phylogenomic databases

OrthoDBiVOG09000186.

Family and domain databases

Gene3Di3.30.380.10. 1 hit.
InterProiView protein in InterPro
IPR002703. Levivir_coat.
IPR015954. Phage_RNA-type_capsid.
PfamiView protein in Pfam
PF01819. Levi_coat. 1 hit.
SUPFAMiSSF55405. SSF55405. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P03612-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASNFTQFVL VDNGGTGDVT VAPSNFANGV AEWISSNSRS QAYKVTCSVR
60 70 80 90 100
QSSAQNRKYT IKVEVPKVAT QTVGGVELPV AAWRSYLNME LTIPIFATNS
110 120 130
DCELIVKAMQ GLLKDGNPIP SAIAANSGIY
Length:130
Mass (Da):13,860
Last modified:January 23, 2007 - v2
Checksum:iABCDD9FD8B188C6A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V00642 mRNA. Translation: CAA23989.1.
PIRiB04222. VCBPM2.
RefSeqiNP_040648.1. NC_001417.2.

Genome annotation databases

GeneIDi1260899.
KEGGivg:1260899.

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.

Entry informationi

Entry nameiCAPSD_BPMS2
AccessioniPrimary (citable) accession number: P03612
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: March 15, 2017
This is version 113 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families