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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).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
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 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 endoplasmic reticulum Source: UniProtKB-KW
  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 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.
InterProiIPR013320. ConA-like_dom.
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

        10         20         30         40         50
MASLIYRQLL TNSYTVNLSD EIQEIGSAKS KNVTINPGPF AQTGYAPVNW
60 70 80 90 100
GAGETNDSTT VEPLLDGPYR PTTFNPPTSY WVLLAPTVEG VVIQGTNNID
110 120 130 140 150
RWLATILIEP NVQTTNRIYN LFGQQVTLSV ENTSQTQWKF IDVSKTTPTG
160 170 180 190 200
SYTQHGPLFS TPKLYAVMKF SGRIYTYNGT TPNATTGYYS TTNYDTVNMT
210 220 230 240 250
LFCDFYIIPR NQEEKCTEYI NHGLPPIQNT RNVVPVSLSA REVVHTRAQV
260 270 280 290 300
NEDIVVSKTS LWKEMQYNRD ITIRFKFDRT IIKAGGLGYK WSEISFKPIT
310 320 330 340 350
YQYTYTRDGE QITAHTTCSV NGVNNFSYNG GSLPTDFAIS RYEVIKENSF
360 370 380 390 400
VYIDYWDDSQ AFRNMVYVRS LAANLNTVTC TGGSYTFALP LGNYPVMTGG
410 420 430 440 450
TVSLHPAGVT LSTQFTDFVS LNSLRFRFRL TVGEPSFSIT RTRVSRLYGL
460 470 480 490 500
PAANPNNQRE YYEISGRFSL ISLVPSNDDY QTPIMNSVTV RQDLERQLGE
510 520 530 540 550
LRDEFNSLSQ QIAMSQLIDL ALLPLDMFSM FSGIKSTIDA AKSMATNVMK
560 570 580 590 600
RFKRSNLASS VSTLTDAMSD AASSVSRSSS IRSIGSSVSA WTEVSTSITD
610 620 630 640 650
ISTTVDTVST QTATIAKRLR LKEIATQTDG MNFDDISAAV LKTKIDKSVQ
660 670 680 690 700
ITPNTLPDIV TEASEKFIPN RTYRVINNDE VFEAGMDGKF FAYRVDTFDE
710 720 730 740 750
IPFDVQKFAD LVTDSPVISA IIDLKTLKNL KDNYGISKQQ AFDLLRSDPK
760 770
VLREFINQNN PIIRNRIENL IMQCRL
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 IPR013320. ConA-like_dom.
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 29, 2014
This is version 30 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