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B1NKS8

- VP6_ROTHL

UniProt

B1NKS8 - VP6_ROTHL

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Protein
Intermediate capsid protein VP6
Gene
N/A
Organism
Rotavirus A (strain Human/Philippines/L26/1987 G12-P1B[4]-I2-R2-C2-M1/M2-A2-N1-T2-E2-H1) (RV-A)
Status
Reviewed - 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.

Sites

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

GO - Molecular functioni

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

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/Philippines/L26/1987 G12-P1B[4]-I2-R2-C2-M1/M2-A2-N1-T2-E2-H1) (RV-A)
Taxonomic identifieri10953 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesReoviridaeSedoreovirinaeRotavirusRotavirus A
Virus hostiHomo sapiens (Human) [TaxID: 9606]
ProteomesiUP000001459: Genome

Subcellular locationi

Virion
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.

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 VP6
PRO_0000368178Add
BLAST

Post-translational modificationi

The N-terminus is blocked By similarity.

Interactioni

Subunit structurei

Homotrimer. Interacts with VP2 By similarity.

Structurei

3D structure databases

ProteinModelPortaliB1NKS8.
SMRiB1NKS8. Positions 1-397.

Family & Domainsi

Sequence similaritiesi

Belongs to the rotavirus VP6 family.

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.

B1NKS8-1 [UniParc]FASTAAdd to Basket

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MDVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIIT MNGNEFQTGG    50
IGNLPTRNWS FDFGLLGTTL LNLDANYVET ARNTIDYFVD FVDNVCMDEM 100
VRESQRNGIA PQSESLRKLS GIKFKRINFD NSSEYIENWN LQNRRQRTGF 150
TFHKPNIFPY SASFTLNRSQ PAHDNLMGTM WLNAGSEIQV AGFDYSCAIN 200
APANIQQFEH IVQLRRVLTT ATITLLPDAE RFSFPRVINS ADGATTWYFN 250
PVILRPNNVE VEFLLNGQII NTYQARFGTI VARNFDTIRL SFQLMRPLNM 300
TPSVAALFPN AQPFGHHATV GLTLRIESAI CESVLADASE TMLANVTSVR 350
QEYAIPVGPV FPPGMNWTDL ITNYSPSRED NLQRVFTVAS IRSMLVK 397
Length:397
Mass (Da):44,832
Last modified:April 29, 2008 - v1
Checksum:i30CD2928F6FAB593
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
DQ146695 Genomic RNA. Translation: ABA34215.1.
EF583036 Genomic RNA. Translation: ABU87845.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
DQ146695 Genomic RNA. Translation: ABA34215.1 .
EF583036 Genomic RNA. Translation: ABU87845.1 .

3D structure databases

ProteinModelPortali B1NKS8.
SMRi B1NKS8. Positions 1-397.
ModBasei Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Family and domain databases

InterProi IPR008980. Capsid_hemagglutn.
IPR001385. Rotavirus_A/C_VP6.
IPR008935. Virus_capsid_a-hlx_vir.
[Graphical view ]
Pfami PF00980. Rota_Capsid_VP6. 1 hit.
[Graphical view ]
ProDomi PD001812. Rota_Capsid_VP6. 1 hit.
[Graphical view ] [Entries sharing at least one domain ]
SUPFAMi SSF48345. SSF48345. 2 hits.
SSF49818. SSF49818. 1 hit.
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. "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_ROTHL
AccessioniPrimary (citable) accession number: B1NKS8
Secondary accession number(s): A3DSK7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: April 29, 2008
Last modified: December 11, 2013
This is version 26 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.

Keywords - Technical termi

Complete proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi