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P04509 (VP6_ROTRF) Reviewed, UniProtKB/Swiss-Prot

Last modified December 11, 2013. Version 83. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Intermediate capsid protein VP6
OrganismRotavirus A (strain Cow/France/RF/1975 G6-P6[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3) (RV-A) [Complete proteome]
Taxonomic identifier10933 [NCBI]
Taxonomic lineageVirusesdsRNA virusesReoviridaeSedoreovirinaeRotavirusRotavirus A
Virus hostBos taurus (Bovine) [TaxID: 9913]

Protein attributes

Sequence length397 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. 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. Ref.3

Subunit structure

Homotrimer. Interacts with VP2. Ref.4

Subcellular location

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 Potential. Ref.3 Ref.4

Post-translational modification

The N-terminus is blocked.

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.

Sequence similarities

Belongs to the rotavirus VP6 family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 397397Intermediate capsid protein VP6
PRO_0000149561

Sites

Metal binding1531Zinc; shared with all trimeric partners

Experimental info

Mutagenesis321Q → E: Complete loss of in vitro DLP transcription activity, no effect on particle assembly. Ref.4
Mutagenesis651L → 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. Ref.4
Mutagenesis701L → A: Loss of in vitro DLP transcriptase activity, no effect on particle assembly; when associated with D-65. Ref.4
Mutagenesis701L → 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. Ref.4
Mutagenesis711L → 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. Ref.4
Mutagenesis1531H → S: Impared homotrimer formation at pH above 7.0. No effect on transcription activity. Ref.5

Secondary structure

................................................................ 397
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P04509 [UniParc].

Last modified May 30, 2000. Version 2.
Checksum: 86CD8739452CA4A7

FASTA39744,843
        10         20         30         40         50         60 
MDVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIIT MNGNEFQTGG IGNLPIRNWN 

        70         80         90        100        110        120 
FDFGLLGTTL LNLDANYVET ARNTIDYFVD FVDNVCMDEM VRESQRNGIA PQSDSLIKLS 

       130        140        150        160        170        180 
GIKFKRINFD NSSEYIENWN LQNRRQRTGF TFHKPNIFPY SASFTLNRSQ PAHDNLMGTM 

       190        200        210        220        230        240 
WLNAGSEIQV AGFDYSCAIN APANTQQFEH IVQLRRVLTT ATITLLPDAE RFSFPRVITS 

       250        260        270        280        290        300 
ADGATTWYFN PVILRPNNVE IEFLLNGQII NTYQARFGTI IARNFDTIRL SFQLMRPPNM 

       310        320        330        340        350        360 
TPAVAALFPN AQPFEHHATV GLTLRIESAV CESVLADASE TMLANVTSVR QEYAIPVGPV 

       370        380        390 
FPPGMNWTDL ITNYSPSRED NLQRVFTVAS IRSMLVK 

« Hide

References

[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).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
K02254 Genomic RNA. Translation: AAC98425.1.
PIRVPXRBR. A04132.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1QHDX-ray1.95A1-397[»]
3GZUelectron microscopy-C/D/E/F/G/H/I/J/K/L/M/N/O1-397[»]
ProteinModelPortalP04509.
SMRP04509. Positions 1-397.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

InterProIPR008980. Capsid_hemagglutn.
IPR001385. Rotavirus_A/C_VP6.
IPR008935. Virus_capsid_a-hlx_vir.
[Graphical view]
PfamPF00980. Rota_Capsid_VP6. 1 hit.
[Graphical view]
ProDomPD001812. Rota_Capsid_VP6. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMSSF48345. SSF48345. 2 hits.
SSF49818. SSF49818. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP04509.

Entry information

Entry nameVP6_ROTRF
AccessionPrimary (citable) accession number: P04509
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references