P04509 · VP6_ROTRF

Function

function

Intermediate capsid protein that self assembles to form an icosahedral capsid with a T=13 symmetry, which consists of 230 trimers of VP6, with channels at each of its five-fold vertices (PubMed:11285213).
This capsid constitutes the middle concentric layer of the viral mature particle (PubMed:11285213).
The innermost VP2 capsid and the intermediate VP6 capsid remain intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nascent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels at the five-fold axes (By similarity).
VP6 is required for the transcription activity of the DLP (PubMed:12097594).

Miscellaneous

The VP6 trimer contains a zinc ion located at the center of the molecule (PubMed:11285213).
The zinc ion is not essential for either trimerization or transcription activity of the DLP. Zinc-depleted VP6 has an increased sensitivity to proteases (PubMed:12610135).

Features

Showing features for binding site.

139750100150200250300350
TypeIDPosition(s)Description
Binding site153Zn2+ (UniProtKB | ChEBI); ligand shared between all trimeric partners
Binding site266Ca2+ (UniProtKB | ChEBI)
Binding site286Ca2+ (UniProtKB | ChEBI)

GO annotations

all annotationsall molecular functionvirus receptor activitydna bindingrna bindingcytoskeletal motor activitycatalytic activitygtpase activitystructural molecule activitytransporter activitycytoskeletal protein bindinglipid bindingcyclase activityantioxidant activityoxidoreductase activitytransferase activityhydrolase activitylyase activityisomerase activityligase activityprotein tag activitycargo receptor activityhistone bindingprotein folding chaperonetranslation regulator activitynutrient reservoir activityreceptor ligand activitymolecular transducer activitymolecular adaptor activitytoxin activitycell adhesion mediator activitymolecular function regulator activityvirus coreceptor activitycatalytic activity, acting on a proteincatalytic activity, acting on dnacatalytic activity, acting on rnamolecular carrier activitytranscription regulator activitygeneral transcription initiation factor activitymolecular sensor activitymolecular sequestering activityatp-dependent activityother molecular functionall biological processmitotic cell cyclecytokinesiscytoplasmic translationimmune system processmuscle system processcirculatory system processrenal system processrespiratory system processcarbohydrate metabolic processgeneration of precursor metabolites and energydna replicationdna repairdna recombinationchromatin organizationdna-templated transcriptionregulation of dna-templated transcriptiontrna metabolic processprotein foldingprotein glycosylationamino acid metabolic processmodified amino acid metabolic processlipid metabolic processvitamin metabolic processsulfur compound metabolic processintracellular protein transportnucleocytoplasmic transportautophagyinflammatory responsemitochondrion organizationcytoskeleton organizationmicrotubule-based movementperoxisome organizationlysosome organizationchromosome segregationcell adhesionestablishment or maintenance of cell polarityprogrammed cell deathphotosynthesismrna metabolic processsnrna metabolic processvesicle-mediated transportreproductive processdigestive system processsignalingcell differentiationprotein catabolic processextracellular matrix organizationregulatory ncrna-mediated gene silencingtelomere organizationcell junction organizationwound healingribosome biogenesiscilium organizationanatomical structure developmentcell motilitynervous system processendocrine processprotein maturationtransmembrane transportnucleobase-containing small molecule metabolic processhepaticobiliary system processmembrane organizationprotein-containing complex assemblycell wall organization or biogenesisnitrogen cycle metabolic processprotein localization to plasma membranedefense response to other organismdetoxificationmeiotic nuclear divisionmitotic nuclear divisionmitochondrial gene expressioncarbohydrate derivative metabolic processother biological processall cellular componentnuclear chromosomeextracellular regionextracellular spacecell wallnucleusnuclear envelopenucleoplasmchromosomenucleolusmitochondrionlysosomeendosomevacuoleperoxisomeendoplasmic reticulumgolgi apparatuslipid dropletmicrotubule organizing centercytosolribosomecytoskeletonplasma membraneciliumplastidthylakoidexternal encapsulating structureextracellular matrixcytoplasmic vesicleorganelleother cellular component
Cell color indicative of number of GO terms
AspectTerm
Cellular ComponentT=13 icosahedral viral capsid
Cellular Componentviral envelope
Cellular Componentviral intermediate capsid
Molecular Functionhost cell surface receptor binding
Molecular Functionmetal ion binding
Molecular Functionstructural molecule activity
Biological Processfusion of virus membrane with host plasma membrane

Keywords

Names & Taxonomy

Protein names

  • Recommended name
    Intermediate capsid protein VP6

Organism names

Accessions

  • Primary accession
    P04509

Proteomes

Subcellular Location

Virion
Note: Component of the intermediate capsid (PubMed:11285213).
Also found in spherical cytoplasmic structures, called virus factories, that appear early after infection and are the site of viral replication and packaging (Potential)

Keywords

Phenotypes & Variants

Features

Showing features for mutagenesis.

TypeIDPosition(s)Description
Mutagenesis32Complete loss of in vitro DLP transcription activity, no effect on particle assembly.
Mutagenesis65Loss of in vitro DLP transcriptase activity, no effect on particle assembly; when associated with A-70 or N-70. Loss of in vitro DLP assembly and transcriptase activity, and almost complete loss of interaction with VP2; when associated with N-71.
Mutagenesis70Loss of in vitro DLP transcriptase activity, no effect on particle assembly; when associated with D-65.
Mutagenesis70Loss of in vitro DLP assembly and transcriptase activity, and almost complete loss of interaction with VP2; when associated with N-71. Loss of in vitro DLP transcriptase activity, no effect on particle assembly; when associated with D-65.
Mutagenesis71Loss of in vitro DLP assembly and transcriptase activity, and almost complete loss of interaction with VP2; when associated with D-65 or N-70.
Mutagenesis153Impaired homotrimer formation at pH above 7.0. No effect on transcription activity or on VP2-VP6 interaction.

PTM/Processing

Features

Showing features for chain.

TypeIDPosition(s)Description
ChainPRO_00001495611-397Intermediate capsid protein VP6

Post-translational modification

The N-terminus is blocked.
Sumoylated with SUMO1 and SUMO2. Sumoylation of viral proteins seems to have a positive role on viral replication.

Keywords

Interaction

Subunit

Homotrimer (PubMed:11285213).
Interacts with the inner capsid protein VP2 (PubMed:11285213, PubMed:12097594).
Interacts with the outer capsid glycoprotein VP7 (PubMed:11285213, PubMed:19487668).
Interacts with the outer capsid protein VP5* (By similarity).

Family & Domains

Features

Showing features for region.

TypeIDPosition(s)Description
Region62-73Interaction with the inner capsid protein VP2

Sequence similarities

Belongs to the rotavirus VP6 family.

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    397
  • Mass (Da)
    44,843
  • Last updated
    2000-05-30 v2
  • Checksum
    86CD8739452CA4A7
MDVLYSLSKTLKDARDKIVEGTLYSNVSDLIQQFNQMIITMNGNEFQTGGIGNLPIRNWNFDFGLLGTTLLNLDANYVETARNTIDYFVDFVDNVCMDEMVRESQRNGIAPQSDSLIKLSGIKFKRINFDNSSEYIENWNLQNRRQRTGFTFHKPNIFPYSASFTLNRSQPAHDNLMGTMWLNAGSEIQVAGFDYSCAINAPANTQQFEHIVQLRRVLTTATITLLPDAERFSFPRVITSADGATTWYFNPVILRPNNVEIEFLLNGQIINTYQARFGTIIARNFDTIRLSFQLMRPPNMTPAVAALFPNAQPFEHHATVGLTLRIESAVCESVLADASETMLANVTSVRQEYAIPVGPVFPPGMNWTDLITNYSPSREDNLQRVFTVASIRSMLVK

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
K02254
EMBL· GenBank· DDBJ
AAC98425.1
EMBL· GenBank· DDBJ
Genomic RNA

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Disclaimer

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