1yuh

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[[Image:1yuh.jpg|left|200px]]<br /><applet load="1yuh" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yuh, resolution 3.0&Aring;" />
 
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'''FAB FRAGMENT'''<br />
 
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==Overview==
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==FAB FRAGMENT==
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Affinity maturation of the immune response to nitrophenol-containing, antigens has been extensively investigated. Significant strides made, during the past several years with the advent of PCR technology have, provided a wealth of biochemical knowledge. Structural investigations of, the phenomena have however been limited. We have determined the, three-dimensional structure of the Fab fragment of 88C6/12, an, anti-4-hydroxy-3-nitrophenyl acetic acid antibody complexed with the, immunizing hapten and with a heteroclitic iodinated hapten. The, crystallographic structure of the complexes reveals that the binding is, stabilized by a number of hydrogen bonds and extensive van der Waals, interactions between the hapten and the antibody. In addition, the Fab, binding pocket contains a region of positive electrostatic potential well, suited for interaction with the predominant resonance form of the, nitrophenyl ring system. The observed heteroclicity towards the iodinated, hapten is not a direct result of iodine-protein interactions, but results, from the enhanced stability in the iodinated ring of the resonance form, that binds the antibody. In addition this investigation provides a, rationale for the strong preference for the substitution in the heavy, chain from the germ-line gene encoded Trp 33 to Leu 33 in the mature, anti-nitrophenol response.
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<StructureSection load='1yuh' size='340' side='right'caption='[[1yuh]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1yuh]] is a 4 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=1YUH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YUH 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]] 3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NP:4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC+ACID'>NP</scene></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=1yuh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yuh OCA], [https://pdbe.org/1yuh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yuh RCSB], [https://www.ebi.ac.uk/pdbsum/1yuh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yuh ProSAT]</span></td></tr>
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</table>
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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/yu/1yuh_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=1yuh 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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Affinity maturation of the immune response to nitrophenol-containing antigens has been extensively investigated. Significant strides made during the past several years with the advent of PCR technology have provided a wealth of biochemical knowledge. Structural investigations of the phenomena have however been limited. We have determined the three-dimensional structure of the Fab fragment of 88C6/12, an anti-4-hydroxy-3-nitrophenyl acetic acid antibody complexed with the immunizing hapten and with a heteroclitic iodinated hapten. The crystallographic structure of the complexes reveals that the binding is stabilized by a number of hydrogen bonds and extensive van der Waals interactions between the hapten and the antibody. In addition, the Fab binding pocket contains a region of positive electrostatic potential well suited for interaction with the predominant resonance form of the nitrophenyl ring system. The observed heteroclicity towards the iodinated hapten is not a direct result of iodine-protein interactions, but results from the enhanced stability in the iodinated ring of the resonance form that binds the antibody. In addition this investigation provides a rationale for the strong preference for the substitution in the heavy chain from the germ-line gene encoded Trp 33 to Leu 33 in the mature anti-nitrophenol response.
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==About this Structure==
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Structural analysis of affinity maturation: the three-dimensional structures of complexes of an anti-nitrophenol antibody.,Yuhasz SC, Parry C, Strand M, Amzel LM Mol Immunol. 1995 Oct;32(14-15):1143-55. PMID:8544863<ref>PMID:8544863</ref>
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1YUH is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NP:'>NP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YUH OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural analysis of affinity maturation: the three-dimensional structures of complexes of an anti-nitrophenol antibody., Yuhasz SC, Parry C, Strand M, Amzel LM, Mol Immunol. 1995 Oct;32(14-15):1143-55. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8544863 8544863]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 1yuh" style="background-color:#fffaf0;"></div>
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[[Category: Amzel, L.M.]]
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[[Category: Parry, C.]]
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[[Category: Strand, M.]]
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[[Category: Yuhasz, S.C.]]
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[[Category: NP]]
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[[Category: anti-nitrophenol]]
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[[Category: immunoglobulin]]
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[[Category: lambda light chain]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 17:12:56 2008''
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==See Also==
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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>
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[[Category: Large Structures]]
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[[Category: Mus musculus]]
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[[Category: Amzel LM]]
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[[Category: Parry C]]
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[[Category: Strand M]]
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[[Category: Yuhasz SC]]

Current revision

FAB FRAGMENT

PDB ID 1yuh

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