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P04509

- VP6_ROTRF

UniProt

P04509 - VP6_ROTRF

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Protein

Intermediate capsid protein VP6

Gene
N/A
Organism
Rotavirus A (strain Cow/France/RF/1975 G6-P6[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3) (RV-A)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

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.1 Publication

Sites

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

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 Cow/France/RF/1975 G6-P6[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3) (RV-A)
Taxonomic identifieri10933 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesReoviridaeSedoreovirinaeRotavirusRotavirus A
Virus hostiBos taurus (Bovine) [TaxID: 9913]
ProteomesiUP000007179: 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 Reviewed prediction.2 Publications

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi32 – 321Q → E: Complete loss of in vitro DLP transcription activity, no effect on particle assembly. 1 Publication
Mutagenesisi65 – 651L → D: Loss 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. 1 Publication
Mutagenesisi70 – 701L → A: Loss of in vitro DLP transcriptase activity, no effect on particle assembly; when associated with D-65. 1 Publication
Mutagenesisi70 – 701L → N: Loss 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. 1 Publication
Mutagenesisi71 – 711L → N: Loss of in vitro DLP assembly and transcriptase activity, and almost complete loss of interaction with VP2; when associated with D-65 or N-70. 1 Publication
Mutagenesisi153 – 1531H → S: Impared homotrimer formation at pH above 7.0. No effect on transcription activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 397397Intermediate capsid protein VP6PRO_0000149561Add
BLAST

Post-translational modificationi

The N-terminus is blocked.

Interactioni

Subunit structurei

Homotrimer. Interacts with VP2.1 Publication

Structurei

Secondary structure

1
397
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 1716
Helixi24 – 263
Helixi28 – 4114
Beta strandi45 – 484
Beta strandi57 – 604
Helixi75 – 10026
Turni105 – 1095
Helixi114 – 1196
Helixi122 – 1276
Helixi134 – 1418
Beta strandi150 – 1545
Beta strandi158 – 16811
Beta strandi177 – 1859
Beta strandi187 – 1948
Turni195 – 2006
Helixi202 – 2043
Beta strandi205 – 22723
Helixi230 – 2323
Beta strandi236 – 2394
Beta strandi246 – 2494
Beta strandi251 – 2533
Beta strandi257 – 2659
Beta strandi268 – 2758
Beta strandi278 – 29518
Helixi302 – 3054
Beta strandi310 – 3123
Beta strandi316 – 33318
Helixi342 – 35211
Beta strandi359 – 3613
Helixi363 – 3653
Helixi367 – 3726
Helixi376 – 39217
Turni393 – 3953

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1QHDX-ray1.95A1-397[»]
3GZUelectron microscopy-C/D/E/F/G/H/I/J/K/L/M/N/O1-397[»]
ProteinModelPortaliP04509.
SMRiP04509. Positions 1-397.

Miscellaneous databases

EvolutionaryTraceiP04509.

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.

P04509-1 [UniParc]FASTAAdd to Basket

« Hide

MDVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIIT MNGNEFQTGG    50
IGNLPIRNWN FDFGLLGTTL LNLDANYVET ARNTIDYFVD FVDNVCMDEM 100
VRESQRNGIA PQSDSLIKLS GIKFKRINFD NSSEYIENWN LQNRRQRTGF 150
TFHKPNIFPY SASFTLNRSQ PAHDNLMGTM WLNAGSEIQV AGFDYSCAIN 200
APANTQQFEH IVQLRRVLTT ATITLLPDAE RFSFPRVITS ADGATTWYFN 250
PVILRPNNVE IEFLLNGQII NTYQARFGTI IARNFDTIRL SFQLMRPPNM 300
TPAVAALFPN AQPFEHHATV GLTLRIESAV CESVLADASE TMLANVTSVR 350
QEYAIPVGPV FPPGMNWTDL ITNYSPSRED NLQRVFTVAS IRSMLVK 397
Length:397
Mass (Da):44,843
Last modified:May 30, 2000 - v2
Checksum:i86CD8739452CA4A7
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
K02254 Genomic RNA. Translation: AAC98425.1.
PIRiA04132. VPXRBR.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
K02254 Genomic RNA. Translation: AAC98425.1 .
PIRi A04132. VPXRBR.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1QHD X-ray 1.95 A 1-397 [» ]
3GZU electron microscopy - C/D/E/F/G/H/I/J/K/L/M/N/O 1-397 [» ]
ProteinModelPortali P04509.
SMRi P04509. Positions 1-397.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P04509.

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. "Cloning of bovine rotavirus (RF strain): nucleotide sequence of the gene coding for the major capsid protein."
    Cohen J., Lefevre F., Estes M.K., Bremont M.
    Virology 138:178-182(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
  2. Cohen J.
    Submitted (DEC-1998) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION.
  3. "Purification and characterization of bovine rotavirus cores."
    Bican P., Cohen J., Charpilienne A., Scherrer R.
    J. Virol. 43:1113-1117(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  4. "Identification of rotavirus VP6 residues located at the interface with VP2 that are essential for capsid assembly and transcriptase activity."
    Charpilienne A., Lepault J., Rey F.A., Cohen J.
    J. Virol. 76:7822-7831(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH VP2, SUBCELLULAR LOCATION, MUTAGENESIS OF GLN-32; LEU-65; LEU-70 AND LEU-71.
  5. "A zinc ion controls assembly and stability of the major capsid protein of rotavirus."
    Erk I., Huet J.-C., Duarte M., Duquerroy S., Rey F.A., Cohen J., Lepault J.
    J. Virol. 77:3595-3601(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: ZINC-BINDING, MUTAGENESIS OF HIS-153.
  6. "Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion."
    Mathieu M., Petitpas I., Navaza J., Lepault J., Kohli E., Pothier P., Prasad B.V.V., Cohen J., Rey F.A.
    EMBO J. 20:1485-1497(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS).

Entry informationi

Entry nameiVP6_ROTRF
AccessioniPrimary (citable) accession number: P04509
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: May 30, 2000
Last modified: December 11, 2013
This is version 83 of the entry and version 2 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.

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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