2oqj: Difference between revisions

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-{{Seed}}
-[[Image:2oqj.png|left|200px]]
-<!--
+==Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1==
-The line below this paragraph, containing "STRUCTURE_2oqj", creates the "Structure Box" on the page.
+<StructureSection load='2oqj' size='340' side='right'caption='[[2oqj]], [[Resolution|resolution]] 2.80&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'>[[2oqj]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OQJ 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]] 2.8&#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=2oqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oqj OCA], [https://pdbe.org/2oqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oqj RCSB], [https://www.ebi.ac.uk/pdbsum/2oqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oqj ProSAT]</span></td></tr>
-{{STRUCTURE_2oqj|  PDB=2oqj  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q6N089_HUMAN Q6N089_HUMAN]
+== 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/oq/2oqj_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=2oqj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+MAb 2G12 neutralizes HIV-1 by binding with high affinity to a cluster of high-mannose oligosaccharides on the envelope glycoprotein, gp120. Screening of phage-displayed peptide libraries with 2G12 identified peptides that bind specifically, with K(d)s ranging from 0.4 to 200 microM. The crystal structure of a 21-mer peptide ligand in complex with 2G12 Fab was determined at 2.8 A resolution. Comparison of this structure with previous structures of 2G12-carbohydrate complexes revealed striking differences in the mechanism of 2G12 binding to peptide vs. carbohydrate. The peptide occupies a site different from, but adjacent to, the primary carbohydrate-binding site on 2G12, and makes only slightly fewer contacts to the Fab than Man(9)GlcNAc(2) (51 vs. 56, respectively). However, only two antibody contacts with the peptide are hydrogen bonds in contrast to six with Man(9)GlcNAc(2), and only three of the antibody residues that interact with Man(9)GlcNAc(2) also contact the peptide. Thus, this mechanism of peptide binding to 2G12 does not support structural mimicry of the native carbohydrate epitope on gp120, since it neither replicates the oligosaccharide footprint on the antibody nor most of the contact residues. Moreover, 2G12.1 peptide is not an immunogenic mimic of the 2G12 epitope, since antisera produced against it did not bind gp120.
-===Crystal structure analysis of Fab 2G12 in complex with peptide 2G12.1===
+A peptide inhibitor of HIV-1 neutralizing antibody 2G12 is not a structural mimic of the natural carbohydrate epitope on gp120.,Menendez A, Calarese DA, Stanfield RL, Chow KC, Scanlan CN, Kunert R, Katinger H, Burton DR, Wilson IA, Scott JK FASEB J. 2008 May;22(5):1380-92. Epub 2008 Jan 15. PMID:18198210<ref>PMID:18198210</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2oqj" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18198210}}, adds the Publication Abstract to the page
+*[[Antibody 3D structures|Antibody 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18198210 is the PubMed ID number.
+*[[3D structures of human antibody|3D structures of human antibody]]
--->
+== References ==
-{{ABSTRACT_PUBMED_18198210}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-OQJ is a 12 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OQJ OCA].
-==Reference==
-<ref group="xtra">PMID:18198210</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Calarese, D A.]]
+[[Category: Large Structures]]
-[[Category: Menendez, A.]]
+[[Category: Calarese DA]]
-[[Category: Scott, J K.]]
+[[Category: Menendez A]]
-[[Category: Stanfield, R L.]]
+[[Category: Scott JK]]
-[[Category: Wilson, I A.]]
+[[Category: Stanfield RL]]
-[[Category: Immune system]]
+[[Category: Wilson IA]]
-[[Category: Immunoglobulin fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:01:12 2009''