1ndm

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[[Image:1ndm.jpg|left|200px]]
 
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==Crystal structure of Fab fragment of antibody HyHEL-26 complexed with lysozyme==
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The line below this paragraph, containing "STRUCTURE_1ndm", creates the "Structure Box" on the page.
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<StructureSection load='1ndm' size='340' side='right'caption='[[1ndm]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1ndm]] 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=1NDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NDM FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ndm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ndm OCA], [https://pdbe.org/1ndm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ndm RCSB], [https://www.ebi.ac.uk/pdbsum/1ndm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ndm ProSAT]</span></td></tr>
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{{STRUCTURE_1ndm| PDB=1ndm | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/IGKC_MOUSE IGKC_MOUSE]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1ndm_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1ndm ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''Crystal structure of Fab fragment of antibody HyHEL-26 complexed with lysozyme'''
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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>
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==Overview==
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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.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1NDM 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=1NDM OCA].
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</div>
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<div class="pdbe-citations 1ndm" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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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]
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*[[Lysozyme 3D structures|Lysozyme 3D structures]]
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*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Gallus gallus]]
[[Category: Gallus gallus]]
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[[Category: Lysozyme]]
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[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
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[[Category: Protein complex]]
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[[Category: Li H]]
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[[Category: Li, H.]]
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[[Category: Li Y]]
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[[Category: Li, Y.]]
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[[Category: Mariuzza RA]]
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[[Category: Mariuzza, R A.]]
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[[Category: Antibody]]
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[[Category: Hyhel-26]]
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[[Category: Lysozyme]]
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[[Category: Mutant]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 02:24:31 2008''
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Current revision

Crystal structure of Fab fragment of antibody HyHEL-26 complexed with lysozyme

PDB ID 1ndm

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