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Entry version 137 (07 Oct 2020)
Sequence version 2 (23 Jan 2007)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionRNA-binding
Biological processTranslation regulation

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Capsid protein
Short name:
CP
Alternative name(s):
Coat protein
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia phage MS2 (Bacteriophage MS2)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri329852 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiVirusesRiboviriaOrthornaviraeLenarviricotaAllassoviricetesLeviviralesLeviviridaeLevivirus
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section only exists in viral entries and indicates the host(s) either as a specific organism or taxonomic group of organisms that are susceptible to be infected by a virus.<p><a href='/help/virus_host' target='_top'>More...</a></p>Virus hostiEscherichia coli [TaxID: 562]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002127 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Genome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Capsid protein, T=3 icosahedral capsid protein, Virion

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>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

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved; by hostBy similarity
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001648432 – 130Capsid proteinAdd BLAST129

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>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

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection">Interaction</a>' section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

P03612
With#Exp.IntAct
itself2EBI-781118,EBI-781118

GO - Molecular functioni

Protein-protein interaction databases

Database of interacting proteins

More...
DIPi
DIP-37669N

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1130
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P03612

Database of comparative protein structure models

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ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P03612

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni32 – 105Viral RNA-binding1 PublicationAdd BLAST74

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the Levivirus capsid protein family.Curated

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.380.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR002703, Levivir_coat
IPR015954, Phage_RNA-type_capsid

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01819, Levi_coat, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF55405, SSF55405, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iABCDD9FD8B188C6A
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
V00642 mRNA Translation: CAA23989.1

Protein sequence database of the Protein Information Resource

More...
PIRi
B04222, VCBPM2

NCBI Reference Sequences

More...
RefSeqi
NP_040648.1, NC_001417.2

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

<p>This subsection of the <a href="http://www.uniprot.org/manual/cross%5Freferences%5Fsection">Cross-references</a> section provides links to various web resources that are relevant for a specific protein.<p><a href='/help/web_resource' target='_top'>More...</a></p>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:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
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[»]
6RRSelectron microscopy3.90A/B/C1-130[»]
6RRTelectron microscopy6.00A/B/C/D1-130[»]
7MSFX-ray2.80A/B/C2-130[»]
SMRiP03612
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

DIPiDIP-37669N

Miscellaneous databases

EvolutionaryTraceiP03612

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

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiCAPSD_BPMS2
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P03612
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: October 7, 2020
This is version 137 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. UniProtKB entry view manual
    User manual for the UniProtKB entry view
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