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Protein

Capsid protein

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

Functioni

Self-assembles to form the T=3 icosahedral virus shell that protects the viral nucleic acid. Acts as a translational repressor by binding with high specificity to a single stem-loop structure in the genomic RNA that contains the initiation codon of the gene for the viral replicase. Involved in virus assembly through the interaction between a capsid protein dimer and the multiple packaging signals present in the RNA genome.6 Publications

GO - Molecular functioni

  • RNA binding Source: UniProtKB
  • structural molecule activity Source: InterPro
Complete GO annotation...

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Capsid protein
Alternative name(s):
Coat protein
OrganismiEnterobacteria 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 opy of the maturation protein.1 Publication1 Publication

GO - Cellular componenti

  • T=3 icosahedral viral capsid Source: UniProtKB
Complete GO annotation...

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

PTM / Processingi

Molecule processing

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

Interactioni

Subunit structurei

Homodimer. The capsid proteins form dimers that assemble by group of 5. Twelve such pentamers are linked together with free dimers.1 Publication

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[»]
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
Regioni43Operator hairpin RNA-binding4 Publications1

Sequence similaritiesi

Belongs to the Levivirus capsid protein family.Curated

Family and domain databases

Gene3Di3.30.380.10. 1 hit.
InterProiIPR002703. Levivir_coat.
IPR015954. Phage_RNA-type_capsid.
[Graphical view]
PfamiPF01819. Levi_coat. 1 hit.
[Graphical view]
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.

Cross-referencesi

Web resourcesi

Virus Particle ExploreR db

Icosahedral capsid structure

Virus Particle ExploreR db

Icosahedral capsid structure assembled from a chemically modified RNA genome hairpin variant

Virus Particle ExploreR db

Icosahedral capsid structure assembled from a modified RNA genome hairpin variant G7

Virus Particle ExploreR db

Icosahedral capsid structure assembled from modified RNA genome hairpin variant G10

Virus Particle ExploreR db

Icosahedral capsid structure assembled from modified RNA genome hairpin variant C10

Virus Particle ExploreR db

Icosahedral capsid structure of mutant E77D

Virus Particle ExploreR db

Icosahedral capsid structure of mutant T60S

Virus Particle ExploreR db

Icosahedral capsid structure of mutant T46A

Virus Particle ExploreR db

Icosahedral capsid structure of mutant T46A

Virus Particle ExploreR db

Icosahedral capsid structure of mutant T60S

Virus Particle ExploreR db

Icosahedral capsid structure of mutant P79N

Virus Particle ExploreR db

Icosahedral capsid structure associated with 8 nt RNA

Virus Particle ExploreR db

Icosahedral capsid structure associated with 19 nt RNA

Virus Particle ExploreR db

Icosahedral capsid structure associated with 19 nt RNA

Virus Particle ExploreR db

Icosahedral capsid structure associated with 23 nt RNA

Virus Particle ExploreR db

Icosahedral capsid structure

Virus Particle ExploreR db

Icosahedral capsid structure associated with a aptamer RNA

Virus Particle ExploreR db

Icosahedral capsid structure associated with a F5 aptamer RNA

Sequence databases

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

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[»]
6MSFX-ray2.80A/B/C2-130[»]
7MSFX-ray2.80A/B/C2-130[»]
ProteinModelPortaliP03612.
SMRiP03612.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-37669N.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1260899.
KEGGivg:1260899.

Miscellaneous databases

EvolutionaryTraceiP03612.

Family and domain databases

Gene3Di3.30.380.10. 1 hit.
InterProiIPR002703. Levivir_coat.
IPR015954. Phage_RNA-type_capsid.
[Graphical view]
PfamiPF01819. Levi_coat. 1 hit.
[Graphical view]
SUPFAMiSSF55405. SSF55405. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiCAPSD_BPMS2
AccessioniPrimary (citable) accession number: P03612
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 111 of the entry and version 2 of the sequence. [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

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.