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Protein

Intermediate capsid protein VP6

Gene
N/A
Organism
Rotavirus A (strain RVA/Cow/France/RF/1975/G6P6[1]) (RV-A)
Status
Reviewed-Annotation score: 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. Nascent 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)DescriptionActionsGraphical viewLength
Metal bindingi153Zinc; shared with all trimeric partners1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Intermediate capsid protein VP6
OrganismiRotavirus A (strain RVA/Cow/France/RF/1975/G6P6[1]) (RV-A)
Taxonomic identifieri10933 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesReoviridaeSedoreovirinaeRotavirusRotavirus A
Virus hostiBos taurus (Bovine) [TaxID: 9913]
Proteomesi
  • UP000007179 Componenti: 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

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Intermediate capsid protein, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi32Q → E: Complete loss of in vitro DLP transcription activity, no effect on particle assembly. 1 Publication1
Mutagenesisi65L → 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 Publication1
Mutagenesisi70L → A: Loss of in vitro DLP transcriptase activity, no effect on particle assembly; when associated with D-65. 1 Publication1
Mutagenesisi70L → 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 Publication1
Mutagenesisi71L → 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 Publication1
Mutagenesisi153H → S: Impaired homotrimer formation at pH above 7.0. No effect on transcription activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001495611 – 397Intermediate capsid protein VP6Add BLAST397

Post-translational modificationi

The N-terminus is blocked.

Interactioni

Subunit structurei

Homotrimer. Interacts with VP2.1 Publication

Structurei

Secondary structure

1397
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi2 – 17Combined sources16
Helixi24 – 26Combined sources3
Helixi28 – 41Combined sources14
Beta strandi45 – 48Combined sources4
Beta strandi57 – 60Combined sources4
Helixi75 – 100Combined sources26
Turni105 – 109Combined sources5
Helixi114 – 119Combined sources6
Helixi122 – 127Combined sources6
Helixi134 – 141Combined sources8
Beta strandi150 – 154Combined sources5
Beta strandi158 – 168Combined sources11
Beta strandi177 – 185Combined sources9
Beta strandi187 – 194Combined sources8
Turni195 – 200Combined sources6
Helixi202 – 204Combined sources3
Beta strandi205 – 227Combined sources23
Helixi230 – 232Combined sources3
Beta strandi236 – 239Combined sources4
Beta strandi246 – 249Combined sources4
Beta strandi251 – 253Combined sources3
Beta strandi257 – 265Combined sources9
Beta strandi268 – 275Combined sources8
Beta strandi278 – 295Combined sources18
Helixi302 – 305Combined sources4
Beta strandi310 – 312Combined sources3
Beta strandi316 – 333Combined sources18
Helixi342 – 352Combined sources11
Beta strandi359 – 361Combined sources3
Helixi363 – 365Combined sources3
Helixi367 – 372Combined sources6
Helixi376 – 392Combined sources17
Turni393 – 395Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1QHDX-ray1.95A1-397[»]
3GZUelectron microscopy-C/D/E/F/G/H/I/J/K/L/M/N/O1-397[»]
3J9Selectron microscopy2.60A1-397[»]
ProteinModelPortaliP04509.
SMRiP04509.
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

        10         20         30         40         50
MDVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIIT MNGNEFQTGG
60 70 80 90 100
IGNLPIRNWN FDFGLLGTTL LNLDANYVET ARNTIDYFVD FVDNVCMDEM
110 120 130 140 150
VRESQRNGIA PQSDSLIKLS GIKFKRINFD NSSEYIENWN LQNRRQRTGF
160 170 180 190 200
TFHKPNIFPY SASFTLNRSQ PAHDNLMGTM WLNAGSEIQV AGFDYSCAIN
210 220 230 240 250
APANTQQFEH IVQLRRVLTT ATITLLPDAE RFSFPRVITS ADGATTWYFN
260 270 280 290 300
PVILRPNNVE IEFLLNGQII 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):44,843
Last modified:May 30, 2000 - v2
Checksum:i86CD8739452CA4A7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K02254 Genomic RNA. Translation: AAC98425.1.
PIRiA04132. VPXRBR.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
K02254 Genomic RNA. Translation: AAC98425.1.
PIRiA04132. VPXRBR.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1QHDX-ray1.95A1-397[»]
3GZUelectron microscopy-C/D/E/F/G/H/I/J/K/L/M/N/O1-397[»]
3J9Selectron microscopy2.60A1-397[»]
ProteinModelPortaliP04509.
SMRiP04509.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP04509.

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...

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: November 30, 2016
This is version 96 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

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 one 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.