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P0C6Y8

- VP4_ROTP3

UniProt

P0C6Y8 - VP4_ROTP3

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
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    • History
      Entry version 29 (01 Oct 2014)
      Sequence version 1 (24 Mar 2009)
      Previous versions | rss
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    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.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.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.By similarity

    Sites

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

    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 Curated
    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

    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 VP4PRO_0000369439Add
    BLAST
    Chaini1 – 231231Outer capsid protein VP8*By similarityPRO_0000369440Add
    BLAST
    Chaini248 – 776529Outer capsid protein VP5*By similarityPRO_0000369441Add
    BLAST

    Amino acid modifications

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

    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.By similarity

    Keywords - PTMi

    Cleavage on pair of basic residues, Disulfide bond, Glycoprotein

    Interactioni

    Subunit structurei

    VP4 is a homotrimer Potential. 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 Potential. 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.By similarityCurated

    Structurei

    Secondary structure

    1
    776
    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[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0C6Y8.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni248 – 480233Antigen domainBy similarityAdd
    BLAST
    Regioni308 – 3103DGE motif
    Regioni389 – 40921Hydrophobic; possible role in virus entry into host cellSequence AnalysisAdd
    BLAST

    Coiled coil

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Coiled coili484 – 51835Sequence AnalysisAdd
    BLAST

    Compositional bias

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

    Sequence similaritiesi

    Belongs to the rotavirus VP4 family.Curated

    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

    « Hide

    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: October 1, 2014
    This is version 29 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