2dwr: Difference between revisions

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[[Image:2dwr.png|left|200px]]


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==Crystal structure of the human Wa rotavirus VP8* carbohydrate-recognising domain==
The line below this paragraph, containing "STRUCTURE_2dwr", creates the "Structure Box" on the page.
<StructureSection load='2dwr' size='340' side='right'caption='[[2dwr]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2dwr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_rotavirus_A Human rotavirus A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DWR FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
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<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=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr>
{{STRUCTURE_2dwr| PDB=2dwr |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dwr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dwr OCA], [https://pdbe.org/2dwr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dwr RCSB], [https://www.ebi.ac.uk/pdbsum/2dwr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dwr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/VP4_ROTHW VP4_ROTHW] 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.  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.  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).
== 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/dw/2dwr_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=2dwr ConSurf].
<div style="clear:both"></div>


===Crystal structure of the human Wa rotavirus VP8* carbohydrate-recognising domain===
==See Also==
 
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
 
__TOC__
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</StructureSection>
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[[Category: Human rotavirus A]]
(as it appears on PubMed at http://www.pubmed.gov), where 17306299 is the PubMed ID number.
[[Category: Large Structures]]
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[[Category: Blanchard H]]
{{ABSTRACT_PUBMED_17306299}}
 
==About this Structure==
2DWR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Human_rotavirus_a Human rotavirus a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWR OCA].
 
==Reference==
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 BS, von Itzstein M, J Mol Biol. 2007 Apr 6;367(4):1215-26. Epub 2007 Jan 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17306299 17306299]
 
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the VP8* carbohydrate-binding protein of the human rotavirus strain Wa., Kraschnefski MJ, Scott SA, Holloway G, Coulson BS, von Itzstein M, Blanchard H, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Nov 1;61(Pt, 11):989-93. Epub 2005 Oct 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16511215 16511215]
[[Category: Human rotavirus a]]
[[Category: Single protein]]
[[Category: Blanchard, H.]]
[[Category: Beta-sandwich]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 23:16:00 2008''

Latest revision as of 09:25, 3 April 2024

Crystal structure of the human Wa rotavirus VP8* carbohydrate-recognising domainCrystal structure of the human Wa rotavirus VP8* carbohydrate-recognising domain

Structural highlights

2dwr is a 1 chain structure with sequence from Human rotavirus A. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VP4_ROTHW 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. 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. 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).

Evolutionary Conservation

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

See Also

2dwr, resolution 2.50Å

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