2ny6: Difference between revisions

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-[[Image:2ny6.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2ny6", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2ny6|  PDB=2ny6  |  SCENE=  }}
-'''HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b'''
+==HIV-1 gp120 Envelope Glycoprotein (M95W, W96C, I109C, T123C, T257S, V275C,S334A, S375W, Q428C, G431C) Complexed with CD4 and Antibody 17b==
+<StructureSection load='2ny6' size='340' side='right'caption='[[2ny6]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ny6]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NY6 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]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=2ny6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ny6 OCA], [https://pdbe.org/2ny6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ny6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ny6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ny6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8Q7Z9_9HIV1 Q8Q7Z9_9HIV1]
+== 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/ny/2ny6_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2ny6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The remarkable diversity, glycosylation and conformational flexibility of the human immunodeficiency virus type 1 (HIV-1) envelope (Env), including substantial rearrangement of the gp120 glycoprotein upon binding the CD4 receptor, allow it to evade antibody-mediated neutralization. Despite this complexity, the HIV-1 Env must retain conserved determinants that mediate CD4 binding. To evaluate how these determinants might provide opportunities for antibody recognition, we created variants of gp120 stabilized in the CD4-bound state, assessed binding of CD4 and of receptor-binding-site antibodies, and determined the structure at 2.3 A resolution of the broadly neutralizing antibody b12 in complex with gp120. b12 binds to a conformationally invariant surface that overlaps a distinct subset of the CD4-binding site. This surface is involved in the metastable attachment of CD4, before the gp120 rearrangement required for stable engagement. A site of vulnerability, related to a functional requirement for efficient association with CD4, can therefore be targeted by antibody to neutralize HIV-1.
-==Overview==
+Structural definition of a conserved neutralization epitope on HIV-1 gp120.,Zhou T, Xu L, Dey B, Hessell AJ, Van Ryk D, Xiang SH, Yang X, Zhang MY, Zwick MB, Arthos J, Burton DR, Dimitrov DS, Sodroski J, Wyatt R, Nabel GJ, Kwong PD Nature. 2007 Feb 15;445(7129):732-7. PMID:17301785<ref>PMID:17301785</ref>
-The remarkable diversity, glycosylation and conformational flexibility of the human immunodeficiency virus type 1 (HIV-1) envelope (Env), including substantial rearrangement of the gp120 glycoprotein upon binding the CD4 receptor, allow it to evade antibody-mediated neutralization. Despite this complexity, the HIV-1 Env must retain conserved determinants that mediate CD4 binding. To evaluate how these determinants might provide opportunities for antibody recognition, we created variants of gp120 stabilized in the CD4-bound state, assessed binding of CD4 and of receptor-binding-site antibodies, and determined the structure at 2.3 A resolution of the broadly neutralizing antibody b12 in complex with gp120. b12 binds to a conformationally invariant surface that overlaps a distinct subset of the CD4-binding site. This surface is involved in the metastable attachment of CD4, before the gp120 rearrangement required for stable engagement. A site of vulnerability, related to a functional requirement for efficient association with CD4, can therefore be targeted by antibody to neutralize HIV-1.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-NY6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NY6 OCA].
+</div>
+<div class="pdbe-citations 2ny6" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural definition of a conserved neutralization epitope on HIV-1 gp120., Zhou T, Xu L, Dey B, Hessell AJ, Van Ryk D, Xiang SH, Yang X, Zhang MY, Zwick MB, Arthos J, Burton DR, Dimitrov DS, Sodroski J, Wyatt R, Nabel GJ, Kwong PD, Nature. 2007 Feb 15;445(7129):732-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17301785 17301785]
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[CD4 3D structures|CD4 3D structures]]
+*[[Gp120 3D structures|Gp120 3D structures]]
+*[[3D structures of human antibody|3D structures of human antibody]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
 [[Category: Human immunodeficiency virus 1]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Arthos, J.]]
+[[Category: Arthos J]]
-[[Category: Burton, D R.]]
+[[Category: Burton DR]]
-[[Category: Dey, B.]]
+[[Category: Dey B]]
-[[Category: Dimitrov, D S.]]
+[[Category: Dimitrov DS]]
-[[Category: Hessell, A J.]]
+[[Category: Hessell AJ]]
-[[Category: Kwong, P D.]]
+[[Category: Kwong PD]]
-[[Category: Nabel, G J.]]
+[[Category: Nabel GJ]]
-[[Category: Ryk, D Van.]]
+[[Category: Sodroski J]]
-[[Category: Sodroski, J.]]
+[[Category: Van Ryk D]]
-[[Category: Wyatt, R.]]
+[[Category: Wyatt R]]
-[[Category: Xiang, S H.]]
+[[Category: Xiang SH]]
-[[Category: Xu, L.]]
+[[Category: Xu L]]
-[[Category: Yang, X.]]
+[[Category: Yang X]]
-[[Category: Zhang, M Y.]]
+[[Category: Zhang MY]]
-[[Category: Zhou, T.]]
+[[Category: Zhou T]]
-[[Category: Zwick, M B.]]
+[[Category: Zwick MB]]
-[[Category: Antibody]]
-[[Category: Cd4]]
-[[Category: Gp120]]
-[[Category: Hiv]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 10:03:54 2008''