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New page: left|200px<br /><applet load="1kqr" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kqr, resolution 1.4Å" /> '''Crystal Structure of ...
 
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[[Image:1kqr.gif|left|200px]]<br /><applet load="1kqr" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1kqr, resolution 1.4&Aring;" />
'''Crystal Structure of the Rhesus Rotavirus VP4 Sialic Acid Binding Domain in Complex with 2-O-methyl-alpha-D-N-acetyl neuraminic acid'''<br />


==Overview==
==Crystal Structure of the Rhesus Rotavirus VP4 Sialic Acid Binding Domain in Complex with 2-O-methyl-alpha-D-N-acetyl neuraminic acid==
Cell attachment and membrane penetration are functions of the rotavirus, outer capsid spike protein, VP4. An activating tryptic cleavage of VP4, produces the N-terminal fragment, VP8*, which is the viral hemagglutinin, and an important target of neutralizing antibodies. We have determined, by, X-ray crystallography, the atomic structure of the VP8* core bound to, sialic acid and, by NMR spectroscopy, the structure of the unliganded VP8*, core. The domain has the beta-sandwich fold of the galectins, a family of, sugar binding proteins. The surface corresponding to the galectin, carbohydrate binding site is blocked, and rotavirus VP8* instead binds, sialic acid in a shallow groove between its two beta-sheets. There appears, to be a small induced fit on binding. The residues that contact sialic, acid are conserved in sialic acid-dependent rotavirus strains., Neutralization escape mutations are widely distributed over the VP8*, surface and cluster in four epitopes. From the fit of the VP8* core into, the virion spikes, we propose that VP4 arose from the insertion of a host, carbohydrate binding domain into a viral membrane interaction protein.
<StructureSection load='1kqr' size='340' side='right'caption='[[1kqr]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1kqr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Simian_rotavirus_A_strain_RRV Simian rotavirus A strain RRV]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KQR FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MNA:2-O-METHYL-5-N-ACETYL-ALPHA-D-+NEURAMINIC+ACID'>MNA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqr OCA], [https://pdbe.org/1kqr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kqr RCSB], [https://www.ebi.ac.uk/pdbsum/1kqr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/VP4_ROTRH VP4_ROTRH] 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. It is subsequently lost, together with VP7, following virus entry into the host cell. Rotavirus attachment and entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. In sialic acid-dependent and/or integrin-dependent strains, VP4 seems to essentially target sialic acid and/or the integrin heterodimer ITGA2/ITGB1.<ref>PMID:20375171</ref>  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.<ref>PMID:20375171</ref>  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.<ref>PMID:20375171</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kq/1kqr_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kqr ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1KQR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhesus_rotavirus Rhesus rotavirus] with SO4, MNA and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KQR OCA].
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
 
== References ==
==Reference==
<references/>
The rhesus rotavirus VP4 sialic acid binding domain has a galectin fold with a novel carbohydrate binding site., Dormitzer PR, Sun ZY, Wagner G, Harrison SC, EMBO J. 2002 Mar 1;21(5):885-97. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11867517 11867517]
__TOC__
[[Category: Rhesus rotavirus]]
</StructureSection>
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Dormitzer, P.R.]]
[[Category: Simian rotavirus A strain RRV]]
[[Category: Harrison, S.C.]]
[[Category: Dormitzer PR]]
[[Category: Sun, Z.Y.J.]]
[[Category: Harrison SC]]
[[Category: Wagner, G.]]
[[Category: Sun Z-YJ]]
[[Category: GOL]]
[[Category: Wagner G]]
[[Category: MNA]]
[[Category: SO4]]
[[Category: cell attachment]]
[[Category: galectin fold]]
[[Category: hemagglutinin]]
[[Category: lectin]]
[[Category: neutralization antigen]]
[[Category: outer capsid]]
[[Category: rotavirus]]
[[Category: sialic acid]]
[[Category: spike protein]]
[[Category: vp4]]
[[Category: vp8*]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:41:08 2007''

Latest revision as of 10:27, 14 February 2024

Crystal Structure of the Rhesus Rotavirus VP4 Sialic Acid Binding Domain in Complex with 2-O-methyl-alpha-D-N-acetyl neuraminic acidCrystal Structure of the Rhesus Rotavirus VP4 Sialic Acid Binding Domain in Complex with 2-O-methyl-alpha-D-N-acetyl neuraminic acid

Structural highlights

1kqr is a 1 chain structure with sequence from Simian rotavirus A strain RRV. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.4Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VP4_ROTRH 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. It is subsequently lost, together with VP7, following virus entry into the host cell. Rotavirus attachment and entry into the host cell probably involves multiple sequential contacts between the outer capsid proteins VP4 and VP7, and the cell receptors. In sialic acid-dependent and/or integrin-dependent strains, VP4 seems to essentially target sialic acid and/or the integrin heterodimer ITGA2/ITGB1.[1] 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.[2] 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.[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Kim IS, Trask SD, Babyonyshev M, Dormitzer PR, Harrison SC. Effect of mutations in VP5 hydrophobic loops on rotavirus cell entry. J Virol. 2010 Jun;84(12):6200-7. doi: 10.1128/JVI.02461-09. Epub 2010 Apr 7. PMID:20375171 doi:http://dx.doi.org/10.1128/JVI.02461-09
  2. ↑ Kim IS, Trask SD, Babyonyshev M, Dormitzer PR, Harrison SC. Effect of mutations in VP5 hydrophobic loops on rotavirus cell entry. J Virol. 2010 Jun;84(12):6200-7. doi: 10.1128/JVI.02461-09. Epub 2010 Apr 7. PMID:20375171 doi:http://dx.doi.org/10.1128/JVI.02461-09
  3. ↑ Kim IS, Trask SD, Babyonyshev M, Dormitzer PR, Harrison SC. Effect of mutations in VP5 hydrophobic loops on rotavirus cell entry. J Virol. 2010 Jun;84(12):6200-7. doi: 10.1128/JVI.02461-09. Epub 2010 Apr 7. PMID:20375171 doi:http://dx.doi.org/10.1128/JVI.02461-09

1kqr, resolution 1.40Å

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