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P0C6Y8

- VP4_ROTP3

UniProt

P0C6Y8 - VP4_ROTP3

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Protein
Outer capsid protein VP4
Gene
N/A
Organism
Rotavirus A (isolate Pig/Australia/CRW-8/1987 G3-P9[7]-I5-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx) (RV-A)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

Spike-forming protein that mediates virion attachment to the host epithelial cell receptors and plays a major role in cell penetration, determination of host range restriction and virulence. Rotavirus entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. According to the considered strain, VP4 seems to essentially target sialic acid and/or the integrin heterodimer ITGA2/ITGB1 By similarity.
Outer capsid protein VP5*: forms the spike "foot" and "body". Acts as a membrane permeabilization protein that mediates release of viral particles from endosomal compartments into the cytoplasm. In integrin-dependent strains, VP5* targets the integrin heterodimer ITGA2/ITGB1 for cell attachment By similarity.
VP8* forms the head of the spikes. It is the viral hemagglutinin and an important target of neutralizing antibodies. In sialic acid-dependent strains, VP8* binds to host cell sialic acid, most probably a ganglioside, providing the initial contact By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei231 – 2322Cleavage By similarity
Sitei247 – 2482Cleavage By similarity

GO - Biological processi

  1. permeabilization of host organelle membrane involved in viral entry into host cell Source: UniProtKB-KW
  2. virion attachment to host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hemagglutinin

Keywords - Biological processi

Host-virus interaction, Viral attachment to host cell, Viral penetration into host cytoplasm, Viral penetration via permeabilization of host membrane, Virus entry into host cell

Names & Taxonomyi

Protein namesi
Recommended name:
Outer capsid protein VP4
Alternative name(s):
Hemagglutinin
Cleaved into the following 2 chains:
OrganismiRotavirus A (isolate Pig/Australia/CRW-8/1987 G3-P9[7]-I5-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx) (RV-A)
Taxonomic identifieri31578 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesReoviridaeSedoreovirinaeRotavirus
Virus hostiSus scrofa (Pig) [TaxID: 9823]

Subcellular locationi

Chain Outer capsid protein VP4 : Virion. Host rough endoplasmic reticulum Reviewed prediction
Note: Immature double-layered particles assembled in the cytoplasm bud across the membrane of the endoplasmic reticulum, acquiring during this process a transient lipid membrane that is modified with the ER resident viral glycoproteins NSP4 and VP7; these enveloped particles also contain VP4. As the particles move towards the interior of the ER cisternae, the transient lipid membrane and the non-structural protein NSP4 are lost, while the virus surface proteins VP4 and VP7 rearrange to form the outermost virus protein layer, yielding mature infectious triple-layered particles.
Chain Outer capsid protein VP8* : Virion
Note: Outer capsid protein By similarity.
Chain Outer capsid protein VP5* : Virion
Note: Outer capsid protein By similarity.

GO - Cellular componenti

  1. host cell rough endoplasmic reticulum Source: UniProtKB-SubCell
  2. viral outer capsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host endoplasmic reticulum, Outer capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 776776Outer capsid protein VP4
PRO_0000369439Add
BLAST
Chaini1 – 231231Outer capsid protein VP8* By similarity
PRO_0000369440Add
BLAST
Chaini248 – 776529Outer capsid protein VP5* By similarity
PRO_0000369441Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi17 – 171N-linked (GlcNAc...); by host Reviewed prediction
Glycosylationi56 – 561N-linked (GlcNAc...); by host Reviewed prediction
Glycosylationi132 – 1321N-linked (GlcNAc...); by host Reviewed prediction
Glycosylationi178 – 1781N-linked (GlcNAc...); by host Reviewed prediction
Glycosylationi183 – 1831N-linked (GlcNAc...); by host Reviewed prediction
Glycosylationi198 – 1981N-linked (GlcNAc...); by host Reviewed prediction
Disulfide bondi203 ↔ 216 Reviewed prediction
Disulfide bondi318 ↔ 380 Reviewed prediction
Glycosylationi325 – 3251N-linked (GlcNAc...); by host Reviewed prediction
Glycosylationi670 – 6701N-linked (GlcNAc...); by host Reviewed prediction

Post-translational modificationi

Proteolytic cleavage by trypsin results in activation of VP4 functions and greatly increases infectivity. The penetration into the host cell is dependent on trypsin treatment of VP4. It produces two peptides, VP5* and VP8* that remain associated with the virion By similarity.

Keywords - PTMi

Cleavage on pair of basic residues, Disulfide bond, Glycoprotein

Interactioni

Subunit structurei

VP4 is a homotrimer Reviewed prediction. VP4 adopts a dimeric appearance above the capsid surface, while forming a trimeric base anchored inside the capsid layer. Only hints of the third molecule are observed above the capsid surface. It probably performs a series of molecular rearrangements during viral entry. Prior to trypsin cleavage, it is flexible. The priming trypsin cleavage triggers its rearrangement into rigid spikes with approximate two-fold symmetry of their protruding parts. After an unknown second triggering event, cleaved VP4 may undergo another rearrangement, in which two VP5* subunits fold back on themselves and join a third subunit to form a tightly associated trimer, shaped like a folded umbrella. VP5* is a homotrimer Reviewed prediction. The trimer is coiled-coil stabilized by its C-terminus, however, its N-terminus, known as antigen domain or "body", seems to be flexible allowing it to self-associate either as a dimer or a trimer. The two- to three-fold reorganization and fold-back of VP5* may be linked to membrane penetration, by exposing its hydrophobic region By similarity.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi66 – 694
Beta strandi71 – 744
Beta strandi80 – 845
Beta strandi88 – 969
Beta strandi98 – 1003
Beta strandi102 – 1087
Beta strandi110 – 12112
Beta strandi124 – 1329
Beta strandi138 – 14710
Beta strandi153 – 16210
Beta strandi165 – 1706
Beta strandi173 – 1808
Beta strandi185 – 1906
Helixi194 – 1963
Beta strandi198 – 2036
Beta strandi205 – 2095
Helixi210 – 2123
Helixi213 – 22210

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2I2SX-ray2.30A/B64-224[»]
3SISX-ray2.20A/B64-224[»]
3SITX-ray1.80A/B64-224[»]
3TAYX-ray1.85A/B64-224[»]

Miscellaneous databases

EvolutionaryTraceiP0C6Y8.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni248 – 480233Antigen domain By similarity
Add
BLAST
Regioni308 – 3103DGE motif
Regioni389 – 40921Hydrophobic; possible role in virus entry into host cell Reviewed prediction
Add
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili484 – 51835 Reviewed prediction
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi560 – 61657Ser-rich
Add
BLAST

Sequence similaritiesi

Belongs to the rotavirus VP4 family.

Keywords - Domaini

Coiled coil

Family and domain databases

Gene3Di2.60.120.200. 1 hit.
InterProiIPR008985. ConA-like_lec_gl_sf.
IPR013320. ConA-like_subgrp.
IPR000416. Haemagglutinin_VP4.
[Graphical view]
PfamiPF00426. VP4_haemagglut. 1 hit.
[Graphical view]
SUPFAMiSSF49899. SSF49899. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0C6Y8-1 [UniParc]FASTAAdd to Basket

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MASLIYRQLL TNSYTVNLSD EIQEIGSAKS KNVTINPGPF AQTGYAPVNW    50
GAGETNDSTT VEPLLDGPYR PTTFNPPTSY WVLLAPTVEG VVIQGTNNID 100
RWLATILIEP NVQTTNRIYN LFGQQVTLSV ENTSQTQWKF IDVSKTTPTG 150
SYTQHGPLFS TPKLYAVMKF SGRIYTYNGT TPNATTGYYS TTNYDTVNMT 200
LFCDFYIIPR NQEEKCTEYI NHGLPPIQNT RNVVPVSLSA REVVHTRAQV 250
NEDIVVSKTS LWKEMQYNRD ITIRFKFDRT IIKAGGLGYK WSEISFKPIT 300
YQYTYTRDGE QITAHTTCSV NGVNNFSYNG GSLPTDFAIS RYEVIKENSF 350
VYIDYWDDSQ AFRNMVYVRS LAANLNTVTC TGGSYTFALP LGNYPVMTGG 400
TVSLHPAGVT LSTQFTDFVS LNSLRFRFRL TVGEPSFSIT RTRVSRLYGL 450
PAANPNNQRE YYEISGRFSL ISLVPSNDDY QTPIMNSVTV RQDLERQLGE 500
LRDEFNSLSQ QIAMSQLIDL ALLPLDMFSM FSGIKSTIDA AKSMATNVMK 550
RFKRSNLASS VSTLTDAMSD AASSVSRSSS IRSIGSSVSA WTEVSTSITD 600
ISTTVDTVST QTATIAKRLR LKEIATQTDG MNFDDISAAV LKTKIDKSVQ 650
ITPNTLPDIV TEASEKFIPN RTYRVINNDE VFEAGMDGKF FAYRVDTFDE 700
IPFDVQKFAD LVTDSPVISA IIDLKTLKNL KDNYGISKQQ AFDLLRSDPK 750
VLREFINQNN PIIRNRIENL IMQCRL 776
Length:776
Mass (Da):86,924
Last modified:March 24, 2009 - v1
Checksum:i149A36C2F637364D
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L07888 mRNA. No translation available.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
L07888 mRNA. No translation available.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2I2S X-ray 2.30 A/B 64-224 [» ]
3SIS X-ray 2.20 A/B 64-224 [» ]
3SIT X-ray 1.80 A/B 64-224 [» ]
3TAY X-ray 1.85 A/B 64-224 [» ]
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P0C6Y8.

Family and domain databases

Gene3Di 2.60.120.200. 1 hit.
InterProi IPR008985. ConA-like_lec_gl_sf.
IPR013320. ConA-like_subgrp.
IPR000416. Haemagglutinin_VP4.
[Graphical view ]
Pfami PF00426. VP4_haemagglut. 1 hit.
[Graphical view ]
SUPFAMi SSF49899. SSF49899. 1 hit.
ProtoNeti Search...

Publicationsi

  1. "Comparative sequence analysis of VP4s from five Australian porcine rotaviruses: implication of an apparent new P type."
    Huang J.A., Nagesha H.S., Holmes I.H.
    Virology 196:319-327(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "Insight into host cell carbohydrate-recognition by human and porcine rotavirus from crystal structures of the virion spike associated carbohydrate-binding domain (VP8*)."
    Blanchard H., Yu X., Coulson B.S., von Itzstein M.
    J. Mol. Biol. 367:1215-1226(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 64-224.

Entry informationi

Entry nameiVP4_ROTP3
AccessioniPrimary (citable) accession number: P0C6Y8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: March 24, 2009
Last modified: February 19, 2014
This is version 28 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

In group A rotaviruses, VP4 defines the P serotype.
This strain has been shown to be sialic acid-dependent, and integrin-independent in cell culture conditions By similarity.

Keywords - Technical termi

3D-structure

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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