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2b4i

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Revision as of 21:27, 19 September 2018

Crystal Structure of the Rhesus Rotavirus VP5 Antigen Domain Trimer

Structural highlights

2b4i is a 3 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1slq, 2b4h
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

The spike protein VP4 is a key component of the membrane penetration apparatus of rotavirus, a nonenveloped virus that causes childhood gastroenteritis. Trypsin cleavage of VP4 produces a fragment, VP5*, with a potential membrane interaction region, and primes rotavirus for cell entry. During entry, the part of VP5* that protrudes from the virus folds back on itself and reorganizes from a local dimer to a trimer. Here, we report that a globular domain of VP5*, the VP5* antigen domain, is an autonomously folding unit that alternatively forms well-ordered dimers and trimers. Because the domain contains heterotypic neutralizing epitopes and is soluble when expressed directly, it is a promising potential subunit vaccine component. X-ray crystal structures show that the dimer resembles the spike body on trypsin-primed virions, and the trimer resembles the folded-back form of the spike. The same structural elements pack differently to form key intermolecular contacts in both oligomers. The intrinsic molecular property of alternatively forming dimers and trimers facilitates the VP5* reorganization, which is thought to mediate membrane penetration during cell entry.

Alternative intermolecular contacts underlie the rotavirus VP5* two- to three-fold rearrangement.,Yoder JD, Dormitzer PR EMBO J. 2006 Apr 5;25(7):1559-68. Epub 2006 Mar 2. PMID:16511559^[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
↑ Yoder JD, Dormitzer PR. Alternative intermolecular contacts underlie the rotavirus VP5* two- to three-fold rearrangement. EMBO J. 2006 Apr 5;25(7):1559-68. Epub 2006 Mar 2. PMID:16511559

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/2b4i"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the Rhesus Rotavirus VP5 Antigen Domain Trimer==
 <StructureSection load='2b4i' size='340' side='right' caption='[[2b4i]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2b4i]] is a 3 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=2B4I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B4I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2b4i]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B4I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B4I FirstGlance]. <br>
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1slq|1slq]], [[2b4h|2b4h]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GENOME 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=2b4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b4i OCA], [http://pdbe.org/2b4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2b4i RCSB], [http://www.ebi.ac.uk/pdbsum/2b4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2b4i 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=2b4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b4i OCA], [http://pdbe.org/2b4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2b4i RCSB], [http://www.ebi.ac.uk/pdbsum/2b4i PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b4/2b4i_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b4/2b4i_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=2b4i ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 30: / Line 30: @@
 ==See Also==
-*[[VP4|VP4]]
 *[[Virus coat protein|Virus coat protein]]
 == References ==
@@ Line 36: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Rotrh]]
 [[Category: Dormitzer, P R]]
 [[Category: Yoder, J D]]

2b4i

From Proteopedia

Revision as of 21:27, 19 September 2018

Crystal Structure of the Rhesus Rotavirus VP5 Antigen Domain Trimer

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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