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Protein

Intermediate capsid protein VP6

Gene
N/A
Organism
Rotavirus A (strain Cow/United Kingdom/UK/1975 G6-P7[5]-I2-R2-C2-M2-A3-N2-T7-E2-H3) (RV-A)
Status
Reviewed-Annotation score: Annotation score: 2 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 (By similarity).By similarity

Sites

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

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/United Kingdom/UK/1975 G6-P7[5]-I2-R2-C2-M2-A3-N2-T7-E2-H3) (RV-A)
Taxonomic identifieri10934 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesReoviridaeSedoreovirinaeRotavirusRotavirus A
Virus hostiBos taurus (Bovine) [TaxID: 9913]
ProteomesiUP000008657 Componenti: Genome

Subcellular locationi

  1. Virion

  2. 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).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 VP6PRO_0000149562Add
BLAST

Post-translational modificationi

The N-terminus is blocked.By similarity

Interactioni

Subunit structurei

Homotrimer. Interacts with VP2 (By similarity).By similarity

Structurei

Secondary structure

1
397
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 1716
Helixi24 – 4118
Beta strandi45 – 484
Beta strandi57 – 604
Helixi75 – 10026
Helixi114 – 1196
Helixi122 – 1276
Helixi134 – 14310
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 strandi241 – 2444
Beta strandi246 – 2494
Beta strandi251 – 2533
Beta strandi257 – 2659
Beta strandi268 – 2758
Beta strandi278 – 29518
Helixi302 – 3076
Beta strandi310 – 3123
Beta strandi316 – 33318
Helixi342 – 35312
Beta strandi359 – 3613
Helixi363 – 3653
Helixi367 – 3726
Helixi376 – 39520

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1M0Xmodel-A1-397[»]
3KZ4X-ray3.80C/D/E/F/G/H/I/J/K/L/M/N/O1-397[»]
ProteinModelPortaliP18610.
SMRiP18610. Positions 1-397.
ModBaseiSearch...
MobiDBiSearch...

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.

P18610-1 [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 PQSDSLRKLS GIKFKRINFD NSSEYIENWN LQNRRQRTGF
160 170 180 190 200
TFHKPNIFPY SASFTLNRSQ PAHDNLMGTM WLNAGSEIQV AGFDYSCAIN
210 220 230 240 250
APANTQQFEH IVQLRRVLTT ATITLLPDAE RFSFPRVINS ADGATTWYFN
260 270 280 290 300
PVILRPNNVE VEFLLNGQII NTYQARFGTI IARNFDTIRL SFQLMRPPNM
310 320 330 340 350
TPAVAALFPN AQPFEHQATV GLTLRIESAV CESVLADASE TMLANVTSVR
360 370 380 390
QEYAIPVGPV FPPGMNWTDL ITNYSPSRED NLQRVFTVAS IRSMLVK
Length:397
Mass (Da):44,876
Last modified:November 1, 1990 - v1
Checksum:i10F65E5FFB71F2AA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X53667 Genomic RNA. Translation: CAA37708.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X53667 Genomic RNA. Translation: CAA37708.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1M0Xmodel-A1-397[»]
3KZ4X-ray3.80C/D/E/F/G/H/I/J/K/L/M/N/O1-397[»]
ProteinModelPortaliP18610.
SMRiP18610. Positions 1-397.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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...

Publicationsi

  1. "Nucleotide sequence of group antigen (VP6) of the UK tissue culture adapted strain of bovine rotavirus."
    Tarlow O., McCrae M.A.
    Nucleic Acids Res. 18:4921-4921(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].

Entry informationi

Entry nameiVP6_ROTBU
AccessioniPrimary (citable) accession number: P18610
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: November 1, 1990
Last modified: January 7, 2015
This is version 75 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).By similarity

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

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 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.