1kqr

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Revision as of 21:23, 19 September 2018

Crystal 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. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	1kri
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.

Publication Abstract from PubMed

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.

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:11867517^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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
↑ 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
↑ 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
↑ Dormitzer PR, Sun ZY, Wagner G, Harrison SC. The rhesus rotavirus VP4 sialic acid binding domain has a galectin fold with a novel carbohydrate binding site. EMBO J. 2002 Mar 1;21(5):885-97. PMID:11867517 doi:10.1093/emboj/21.5.885

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1kqr"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the Rhesus Rotavirus VP4 Sialic Acid Binding Domain in Complex with 2-O-methyl-alpha-D-N-acetyl neuraminic acid==
 <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 [http://en.wikipedia.org/wiki/Rotrh Rotrh]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KQR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1kqr]] is a 1 chain structure. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KQR FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kri|1kri]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">segment 4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10969 ROTRH])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqr OCA], [http://pdbe.org/1kqr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kqr RCSB], [http://www.ebi.ac.uk/pdbsum/1kqr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqr ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kqr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqr OCA], [http://pdbe.org/1kqr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kqr RCSB], [http://www.ebi.ac.uk/pdbsum/1kqr PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kq/1kqr_consurf.spt"</scriptWhenChecked>
+    <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[VP4|VP4]]
+*[[Virus coat protein|Virus coat protein]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Rotrh]]
 [[Category: Dormitzer, P R]]
 [[Category: Harrison, S C]]

1kqr

From Proteopedia

Revision as of 21:23, 19 September 2018

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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