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P04509

- VP6_ROTRF

UniProt

P04509 - VP6_ROTRF

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
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    • History
      Entry version 84 (01 Oct 2014)
      Sequence version 2 (30 May 2000)
      Previous versions | rss
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    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

    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 2 Publications
    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 Potential.Curated

    GO - Cellular componenti

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

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04509.

    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.

    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: October 1, 2014
    This is version 84 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