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Protein

Intermediate capsid protein VP6

Gene
N/A
Organism
Rotavirus A (strain Human/Indonesia/69M/1980 G8-P4[10]-I2-R2-C2-M2-A2-N2-T2-E2-H2) (RV-A)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

Functioni

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. This capsid constitutes the middle concentric layer of the viral mature particle. 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. Nacent transcripts are transcribed within the structural confines of this double-layered particle (DLP) and are extruded through the channels at the five-fold axes. VP6 is required for the transcription activity of the DLP (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi153 – 1531Zinc; shared with all trimeric partnersBy similarity

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. structural molecule activity Source: InterPro

GO - Biological processi

  1. fusion of virus membrane with host plasma membrane Source: InterPro
Complete GO annotation...

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Intermediate capsid protein VP6
OrganismiRotavirus A (strain Human/Indonesia/69M/1980 G8-P4[10]-I2-R2-C2-M2-A2-N2-T2-E2-H2) (RV-A)
Taxonomic identifieri10947 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesReoviridaeSedoreovirinaeRotavirusRotavirus A
Virus hostiHomo sapiens (Human) [TaxID: 9606]
ProteomesiUP000001455 Componenti: Genome

Subcellular locationi

  1. Virion

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

GO - Cellular componenti

  1. viral envelope Source: InterPro
  2. viral intermediate capsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Intermediate capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 397397Intermediate capsid protein VP6PRO_0000368175Add
BLAST

Post-translational modificationi

The N-terminus is blocked.By similarity

Interactioni

Subunit structurei

Homotrimer. Interacts with VP2 (By similarity).By similarity

Family & Domainsi

Sequence similaritiesi

Belongs to the rotavirus VP6 family.Curated

Family and domain databases

InterProiIPR008980. Capsid_hemagglutn.
IPR001385. Rotavirus_A/C_VP6.
IPR008935. Virus_capsid_a-hlx_vir.
[Graphical view]
PfamiPF00980. Rota_Capsid_VP6. 1 hit.
[Graphical view]
ProDomiPD001812. Rota_Capsid_VP6. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF48345. SSF48345. 2 hits.
SSF49818. SSF49818. 1 hit.

Sequencei

Sequence statusi: Complete.

B1NKQ8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIIT MNGTEFQTGG
60 70 80 90 100
IGNLPIRNWN FGFGLLGTTL LNLDANYVET ARNTIDYFVD FVDNVCMDEM
110 120 130 140 150
VRESQRNGIA PQSDSLRKLS GIKFKRINFD NSSEYIENWN LQNRRQRTGF
160 170 180 190 200
TFHKPNIFPY SASFTLNRSQ PAHDNLMGTM WLNAGSEIQV AGFDYSCAIN
210 220 230 240 250
APANTQQFEH IVQLRRVLTT ATITLLPDAE RFSFPRVINS ADGATTWYFN
260 270 280 290 300
PVILRPNNVE VEFLLNGQII NTYQARFGTI IARNFDTIRL SFQLMRPPNM
310 320 330 340 350
TPAVAALFPN AQPFEHHATV GLTLRIESAV CESVLADASE TMLANVTSVR
360 370 380 390
QEYAIPVGPV FPPGMNWTDL ITNYSPSRED NLQRVFTVAS IRSMLVK
Length:397
Mass (Da):44,814
Last modified:April 29, 2008 - v1
Checksum:i4B876883EA5E63C1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EF583016 Genomic RNA. Translation: ABU87825.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EF583016 Genomic RNA. Translation: ABU87825.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

InterProiIPR008980. Capsid_hemagglutn.
IPR001385. Rotavirus_A/C_VP6.
IPR008935. Virus_capsid_a-hlx_vir.
[Graphical view]
PfamiPF00980. Rota_Capsid_VP6. 1 hit.
[Graphical view]
ProDomiPD001812. Rota_Capsid_VP6. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF48345. SSF48345. 2 hits.
SSF49818. SSF49818. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Full genome-based classification of rotaviruses reveals a common origin between human Wa-Like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains."
    Matthijnssens J., Ciarlet M., Heiman E.M., Arijs I., Delbeke T., McDonald S.M., Palombo E.A., Iturriza-Gomara M., Maes P., Patton J.T., Rahman M., Van Ranst M.
    J. Virol. 82:3204-3219(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Entry informationi

Entry nameiVP6_ROTH6
AccessioniPrimary (citable) accession number: B1NKQ8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: April 29, 2008
Last modified: January 7, 2015
This is version 27 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

The zinc ion is not essential for either trimerization or transcription activity of the DLP. Zinc-depleted VP6 has an increased sensitivity to proteases (By similarity).By similarity

Keywords - Technical termi

Complete proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.