2dbl: Difference between revisions

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-{{Seed}}
-[[Image:2dbl.png|left|200px]]
-<!--
+==MOLECULAR BASIS OF CROSS-REACTIVITY AND THE LIMITS OF ANTIBODY-ANTIGEN COMPLEMENTARITY==
-The line below this paragraph, containing "STRUCTURE_2dbl", creates the "Structure Box" on the page.
+<StructureSection load='2dbl' size='340' side='right'caption='[[2dbl]], [[Resolution|resolution]] 2.90&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'>[[2dbl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DBL 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]] 2.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=S5H:5-ALPHA-PREGNANE-3-BETA-OL-HEMISUCCINATE'>S5H</scene></td></tr>
-{{STRUCTURE_2dbl|  PDB=2dbl  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dbl OCA], [https://pdbe.org/2dbl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dbl RCSB], [https://www.ebi.ac.uk/pdbsum/2dbl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dbl ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IGHG1_MOUSE IGHG1_MOUSE]
+== 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/db/2dbl_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=2dbl ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Two major unanswered questions concerning the specificity of antibodies are: how do structurally different antigens bind with high affinity to the same antibody, and what are the limits of the antibody combining site complementarity and flexibility that contribute to such crossreactivity? We report here a comparative analysis of the X-ray structures of five conformationally different steroids in complex with the Fab' fragment of an anti-progesterone antibody DB3 at 2.7 A. This antibody is unable to complement completely the shape of the hydrophobic antigen so that crossreactivity occurs with other ligands without major structural rearrangements of the binding site. Antigen specificity can be explained through conserved interactions of DB3 with the steroid D-ring, whereas some of the crossreactivity is realized through different binding orientations of the steroid skeleton that place the A-ring into alternative pockets on the antibody surface. The restricted gene usage of the VGAM3.8 family in the generation of anti-progesterone monoclonal antibodies may be explained by the specific interaction of VH hallmark residues with the steroid D-ring. This first detailed structure of steroid interactions with a protein could be applied to the understanding of general mechanisms of steroid recognition as well as in the design of specific binding sites for small hydrophobic ligands.
-===MOLECULAR BASIS OF CROSS-REACTIVITY AND THE LIMITS OF ANTIBODY-ANTIGEN COMPLEMENTARITY===
+Molecular basis of crossreactivity and the limits of antibody-antigen complementarity.,Arevalo JH, Taussig MJ, Wilson IA Nature. 1993 Oct 28;365(6449):859-63. PMID:8413674<ref>PMID:8413674</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2dbl" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_8413674}}, adds the Publication Abstract to the page
+*[[Antibody 3D structures|Antibody 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 8413674 is the PubMed ID number.
+*[[Sandbox 20009|Sandbox 20009]]
--->
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
-{{ABSTRACT_PUBMED_8413674}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-DBL is a 2 chains structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DBL OCA].
+</StructureSection>
+[[Category: Large Structures]]
-==Reference==
+[[Category: Mus musculus]]
-<ref group="xtra">PMID:8413674</ref><references group="xtra"/>
+[[Category: Arevalo JH]]
-[[Category: Arevalo, J H.]]
+[[Category: Wilson IA]]
-[[Category: Wilson, I A.]]
-[[Category: Immunoglobulin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:56:34 2009''