1ndg: Difference between revisions

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-[[Image:1ndg.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1ndg", 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.
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-{{STRUCTURE_1ndg|  PDB=1ndg  |  SCENE=  }}
-'''Crystal structure of Fab fragment of antibody HyHEL-8 complexed with its antigen lysozyme'''
+==Crystal structure of Fab fragment of antibody HyHEL-8 complexed with its antigen lysozyme==
+<StructureSection load='1ndg' size='340' side='right'caption='[[1ndg]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ndg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NDG 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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</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=1ndg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ndg OCA], [https://pdbe.org/1ndg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ndg RCSB], [https://www.ebi.ac.uk/pdbsum/1ndg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ndg ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IGKC_MOUSE IGKC_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/nd/1ndg_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=1ndg ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The process whereby the immune system generates antibodies of higher affinities during a response to antigen (affinity maturation) is a prototypical example of molecular evolution. Earlier studies have been confined to antibodies specific for small molecules (haptens) rather than for proteins. We compare the structures of four antibodies bound to the same site on hen egg white lysozyme (HEL) at different stages of affinity maturation. These X-ray snapshots reveal that binding is enhanced, not through the formation of additional hydrogen bonds or van der Waals contacts or by an increase in total buried surface, but by burial of increasing amounts of apolar surface at the expense of polar surface, accompanied by improved shape complementarity. The increase in hydrophobic interactions results from highly correlated rearrangements in antibody residues at the interface periphery, adjacent to the central energetic hot spot. This first visualization of the maturation of antibodies to protein provides insights into the evolution of high affinity in other protein-protein interfaces.
-==Overview==
+X-ray snapshots of the maturation of an antibody response to a protein antigen.,Li Y, Li H, Yang F, Smith-Gill SJ, Mariuzza RA Nat Struct Biol. 2003 Jun;10(6):482-8. PMID:12740607<ref>PMID:12740607</ref>
-The process whereby the immune system generates antibodies of higher affinities during a response to antigen (affinity maturation) is a prototypical example of molecular evolution. Earlier studies have been confined to antibodies specific for small molecules (haptens) rather than for proteins. We compare the structures of four antibodies bound to the same site on hen egg white lysozyme (HEL) at different stages of affinity maturation. These X-ray snapshots reveal that binding is enhanced, not through the formation of additional hydrogen bonds or van der Waals contacts or by an increase in total buried surface, but by burial of increasing amounts of apolar surface at the expense of polar surface, accompanied by improved shape complementarity. The increase in hydrophobic interactions results from highly correlated rearrangements in antibody residues at the interface periphery, adjacent to the central energetic hot spot. This first visualization of the maturation of antibodies to protein provides insights into the evolution of high affinity in other protein-protein interfaces.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-NDG is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NDG OCA].
+</div>
+<div class="pdbe-citations 1ndg" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-X-ray snapshots of the maturation of an antibody response to a protein antigen., Li Y, Li H, Yang F, Smith-Gill SJ, Mariuzza RA, Nat Struct Biol. 2003 Jun;10(6):482-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12740607 12740607]
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Gallus gallus]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Protein complex]]
+[[Category: Li H]]
-[[Category: Li, H.]]
+[[Category: Li Y]]
-[[Category: Li, Y.]]
+[[Category: Mariuzza RA]]
-[[Category: Mariuzza, R A.]]
+[[Category: Smith-Gill SJ]]
-[[Category: Smith-Gill, S J.]]
+[[Category: Yang F]]
-[[Category: Yang, F.]]
-[[Category: Antibody]]
-[[Category: Hyhel-8]]
-[[Category: Lysozyme]]
-[[Category: Mutant]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 02:24:12 2008''