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P12976 (VP4_ROTS1) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 96. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Outer capsid protein VP4
Alternative name(s):
Hemagglutinin

Cleaved into the following 2 chains:

  1. Outer capsid protein VP8*
  2. Outer capsid protein VP5*
OrganismRotavirus A (strain SA11-Both G3-P5B[2]-I2-R2-C5-M5-A5-N2-T5-E2-H5) (RV-A) (Simian Agent 11 (strain Both)) [Complete proteome]
Taxonomic identifier37137 [NCBI]
Taxonomic lineageVirusesdsRNA virusesReoviridaeSedoreovirinaeRotavirusRotavirus A
Virus hostMacaca mulatta (Rhesus macaque) [TaxID: 9544]

Protein attributes

Sequence length776 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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.

Subunit structure

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. Interacts with host ITGA2 (via ITAG2 I-domain); this interaction occurs when ITGA2 is part of the integrin heterodimer ITGA2/ITGB1. Interacts with host integrin heterodimer ITGA4/ITGB1 and ITGA4/ITGB7 By similarity. Ref.2 Ref.3

Subcellular location

Outer capsid protein VP4: Virion. Host rough endoplasmic reticulum Potential. 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.

Outer capsid protein VP8*: Virion. Note: Outer capsid protein By similarity.

Outer capsid protein VP5*: Virion. Note: Outer capsid protein By similarity.

Post-translational modification

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.

Miscellaneous

In group A rotaviruses, VP4 defines the P serotype.

This strain has been shown to be sialic acid-dependent, and integrin-dependent in cell culture conditions By similarity.

Sequence similarities

Belongs to the rotavirus VP4 family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 776776Outer capsid protein VP4
PRO_0000041114
Chain1 – 231231Outer capsid protein VP8* By similarity
PRO_0000041115
Chain248 – 776529Outer capsid protein VP5* By similarity
PRO_0000041116

Regions

Region248 – 480233Antigen domain By similarity
Region308 – 3103DGE motif; interaction with ITGA2/ITGB1 heterodimer By similarity
Region389 – 40921Hydrophobic; possible role in virus entry into host cell Potential
Coiled coil484 – 51835 Potential
Motif308 – 3103DGE motif; interaction with ITGA2/ITGB1 heterodimer Probable
Compositional bias560 – 61657Ser-rich

Sites

Site231 – 2322Cleavage By similarity
Site247 – 2482Cleavage By similarity

Amino acid modifications

Glycosylation321N-linked (GlcNAc...); by host Potential
Glycosylation561N-linked (GlcNAc...); by host Potential
Glycosylation971N-linked (GlcNAc...); by host Potential
Glycosylation1161N-linked (GlcNAc...); by host Potential
Glycosylation1321N-linked (GlcNAc...); by host Potential
Glycosylation1491N-linked (GlcNAc...); by host Potential
Glycosylation1981N-linked (GlcNAc...); by host Potential
Glycosylation3861N-linked (GlcNAc...); by host Potential
Disulfide bond203 ↔ 216 Potential
Disulfide bond318 ↔ 380 Potential

Sequences

Sequence LengthMass (Da)Tools
P12976 [UniParc].

Last modified October 1, 1989. Version 1.
Checksum: EA9B43CE96CC53CF

FASTA77686,775
        10         20         30         40         50         60 
MASLIYRQLL TNSYTVDLSD EIQEIGSTKS QNVTINPGPF AQTGYAPVNW GPGEINDSTT 

        70         80         90        100        110        120 
VEPLLDGPYQ PTTFNPPVDY WMLLAPTTPG VIVEGTNNTD RWLATILIEP NVQSENRTYT 

       130        140        150        160        170        180 
IFGIQEQLTV SNTSQDQWKF IDVVKTTANG SIGQYGPLLS SPKLYAVMKH NEKLYTYEGQ 

       190        200        210        220        230        240 
TPNARTAHYS TTNYDSVNMT AFCDFYIIPR SEESKCTEYI NNGLPPIQNT RNVVPLSLTA 

       250        260        270        280        290        300 
RDVIHYRAQA NEDIVISKTS LWKEMQYNRD ITIRFKFANT IIKSGGLGYK WSEISFKPAN 

       310        320        330        340        350        360 
YQYTYTRDGE EVTAHTTCSV NGVNDFSFNG GYLPTDFVVS KFEVIKENSY VYIDYWDDSQ 

       370        380        390        400        410        420 
AFRNVVYVRS LAANLNSVMC TGGSYNFSLP VGQWPVLTGG AVSLHSAGVT LSTQFTDFVS 

       430        440        450        460        470        480 
LNSLRFRFRL AVEEPHFKLT RTRLDRLYGL PAADPNNGKE YYEIAGRFSL ISLVPSNDDY 

       490        500        510        520        530        540 
QTPIANSVTV RQDLERQLGE LREEFNALSQ EIAMSQLIDL ALLPLDMFSM FSGIKSTIDA 

       550        560        570        580        590        600 
AKSMATNVMK KFKKSGLANS VSTLTDSLSD AASSISRGSS IRSIGSSASA WTDVSTQITD 

       610        620        630        640        650        660 
ISSSVSSVST QTSTISRRLR LKEMATQTEG MNFDDISAAV LKTKIDKSTQ ISPNTIPDIV 

       670        680        690        700        710        720 
TEASEKFIPN RAYRVINNDD VFEAGIDGKF FAYKVDTFEE IPFDVQKFAD LVTDSPVISA 

       730        740        750        760        770 
IIDFKTLKNL NDNYGITKQQ AFNLLRSDPR VLREFINQDN PIIRNRIEQL IMQCRL 

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References

[1]"Complete nucleotide sequence of the simian rotavirus SA11 VP4 gene."
Mitchell D.B., Both G.W.
Nucleic Acids Res. 17:2122-2122(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Integrin-using rotaviruses bind alpha2beta1 integrin alpha2 I domain via VP4 DGE sequence and recognize alphaXbeta2 and alphaVbeta3 by using VP7 during cell entry."
Graham K.L., Halasz P., Tan Y., Hewish M.J., Takada Y., Mackow E.R., Robinson M.K., Coulson B.S.
J. Virol. 77:9969-9978(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH HUMAN INTEGRIN ITGA2.
[3]"Rotaviruses interact with alpha4beta7 and alpha4beta1 integrins by binding the same integrin domains as natural ligands."
Graham K.L., Fleming F.E., Halasz P., Hewish M.J., Nagesha H.S., Holmes I.H., Takada Y., Coulson B.S.
J. Gen. Virol. 86:3397-3408(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH HUMAN INTEGRIN HETERODIMER ITGA4/ITGB1, INTERACTION WITH HUMAN INTEGRIN HETERODIMER ITGA4/ITGB7.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X14204 mRNA. Translation: CAA32420.1.
PIRS03611.

3D structure databases

ProteinModelPortalP12976.
SMRP12976. Positions 64-224, 253-522.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D2.60.120.200. 1 hit.
InterProIPR008985. ConA-like_lec_gl_sf.
IPR013320. ConA-like_subgrp.
IPR000416. Haemagglutinin_VP4.
[Graphical view]
PfamPF00426. VP4_haemagglut. 1 hit.
[Graphical view]
SUPFAMSSF49899. SSF49899. 1 hit.
ProtoNetSearch...

Entry information

Entry nameVP4_ROTS1
AccessionPrimary (citable) accession number: P12976
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: February 19, 2014
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families