1u93: Difference between revisions

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-[[Image:1u93.jpg|left|200px]]
-<!--
+==Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with gp41 Peptide Analog EQDKW-[Dap]-S (cyclic)==
-The line below this paragraph, containing "STRUCTURE_1u93", creates the "Structure Box" on the page.
+<StructureSection load='1u93' size='340' side='right'caption='[[1u93]], [[Resolution|resolution]] 2.37&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'>[[1u93]] is a 3 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=1U93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U93 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]] 2.37&#8491;</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=1u93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u93 OCA], [https://pdbe.org/1u93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u93 RCSB], [https://www.ebi.ac.uk/pdbsum/1u93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u93 ProSAT]</span></td></tr>
-{{STRUCTURE_1u93|  PDB=1u93  |  SCENE=  }}
+</table>
+== 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/u9/1u93_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=1u93 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The quest to create a human immunodeficiency virus type 1 (HIV-1) vaccine capable of eliciting broadly neutralizing antibodies against Env has been challenging. Among other problems, one difficulty in creating a potent immunogen resides in the substantial overall sequence variability of the HIV envelope protein. The membrane-proximal region (MPER) of gp41 is a particularly conserved tryptophan-rich region spanning residues 659 to 683, which is recognized by three broadly neutralizing monoclonal antibodies (bnMAbs), 2F5, Z13, and 4E10. In this study, we first describe the variability of residues in the gp41 MPER and report on the invariant nature of 15 out of 25 amino acids comprising this region. Subsequently, we evaluate the ability of the bnMAb 2F5 to recognize 31 varying sequences of the gp41 MPER at a molecular level. In 19 cases, resulting crystal structures show the various MPER peptides bound to the 2F5 Fab'. A variety of amino acid substitutions outside the 664DKW666 core epitope are tolerated. However, changes at the 664DKW666 motif itself are restricted to those residues that preserve the aspartate's negative charge, the hydrophobic alkyl-pi stacking arrangement between the beta-turn lysine and tryptophan, and the positive charge of the former. We also characterize a possible molecular mechanism of 2F5 escape by sequence variability at position 667, which is often observed in HIV-1 clade C isolates. Based on our results, we propose a somewhat more flexible molecular model of epitope recognition by bnMAb 2F5, which could guide future attempts at designing small-molecule MPER-like vaccines capable of eliciting 2F5-like antibodies.
-'''Crystal structure of the HIV-1 Cross Neutralizing Monoclonal Antibody 2F5 in complex with gp41 Peptide Analog EQDKW-[Dap]-S (cyclic)'''
+Crystallographic definition of the epitope promiscuity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5: vaccine design implications.,Bryson S, Julien JP, Hynes RC, Pai EF J Virol. 2009 Nov;83(22):11862-75. Epub 2009 Sep 9. PMID:19740978<ref>PMID:19740978</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1u93" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U93 OCA].
+*[[Antibody 3D structures|Antibody 3D structures]]
-[[Category: Bryson, S.]]
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-[[Category: Cunningham, A.]]
+*[[3D structures of human antibody|3D structures of human antibody]]
-[[Category: Dong, A.]]
+== References ==
-[[Category: Hynes, R C.]]
+<references/>
-[[Category: Julien, J P.]]
+__TOC__
-[[Category: Katinger, H.]]
+</StructureSection>
-[[Category: Klein, M.]]
+[[Category: Homo sapiens]]
-[[Category: Kunert, R.]]
+[[Category: Human immunodeficiency virus 1]]
-[[Category: Pai, E F.]]
+[[Category: Large Structures]]
-[[Category: Fab complex]]
+[[Category: Bryson S]]
-[[Category: Gp41 peptide]]
+[[Category: Hynes RC]]
-[[Category: Hiv-1 neutralization]]
+[[Category: Julien J-P]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 10:55:09 2008''
+[[Category: Pai EF]]