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New page: left|200px<br /> <applet load="1kfa" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kfa, resolution 2.80Å" /> '''Crystal structure o...
 
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[[Image:1kfa.gif|left|200px]]<br />
<applet load="1kfa" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1kfa, resolution 2.80&Aring;" />
'''Crystal structure of Fab fragment complexed with gibberellin A4'''<br />


==Overview==
==Crystal structure of Fab fragment complexed with gibberellin A4==
Gibberellins, a class of plant hormones, consist of more than 120 members., Only a few of them are recognized by a receptor that remains unknown. The, haptenic mouse monoclonal antibody, 4-B8(8)/E9, was generated against, gibberellin A(4) (GA(4)) to recognize biologically active GA selectivity, and we attempted to confirm the binding properties between the antibody, and GA(4). We carried out an X-ray crystallographic analysis of the, 4-B8(8)/E9 Fab fragment complexed with GA(4) at a 2.8 A resolution by, using the molecular replacement method. The crystal structure of the Fab, fragment showed the typical immunoglobulin fold of the beta-barrel, structure which is the common motif of all antibodies. A small, hapten-combining site was made up of three heavy chain CDR loops. On the, other hand, CDRs of the light chain did not interact directly with GA(4)., The C/D rings of the GA(4) molecule were in van der Waals contact mainly, with the aromatic side chain of Tyr100AH and Phe100BH of CDR-H3. The 3, beta-hydroxyl and 6 beta-carboxyl groups were, respectively, hydrogen-bonded to the main chain of Ala33H and to the Thr53H heavy chain.
<StructureSection load='1kfa' size='340' side='right'caption='[[1kfa]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1kfa]] 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=1KFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KFA 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]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GA4:GIBBERELLIN+A4'>GA4</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=1kfa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kfa OCA], [https://pdbe.org/1kfa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kfa RCSB], [https://www.ebi.ac.uk/pdbsum/1kfa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kfa ProSAT]</span></td></tr>
</table>
== 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/kf/1kfa_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=1kfa ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Gibberellins, a class of plant hormones, consist of more than 120 members. Only a few of them are recognized by a receptor that remains unknown. The haptenic mouse monoclonal antibody, 4-B8(8)/E9, was generated against gibberellin A(4) (GA(4)) to recognize biologically active GA selectivity, and we attempted to confirm the binding properties between the antibody and GA(4). We carried out an X-ray crystallographic analysis of the 4-B8(8)/E9 Fab fragment complexed with GA(4) at a 2.8 A resolution by using the molecular replacement method. The crystal structure of the Fab fragment showed the typical immunoglobulin fold of the beta-barrel structure which is the common motif of all antibodies. A small hapten-combining site was made up of three heavy chain CDR loops. On the other hand, CDRs of the light chain did not interact directly with GA(4). The C/D rings of the GA(4) molecule were in van der Waals contact mainly with the aromatic side chain of Tyr100AH and Phe100BH of CDR-H3. The 3 beta-hydroxyl and 6 beta-carboxyl groups were, respectively, hydrogen-bonded to the main chain of Ala33H and to the Thr53H heavy chain.


==About this Structure==
Crystal structure of the liganded anti-gibberellin A(4) antibody 4-B8(8)/E9 Fab fragment.,Murata T, Fushinobu S, Nakajima M, Asami O, Sassa T, Wakagi T, Yamaguchi I Biochem Biophys Res Commun. 2002 Apr 26;293(1):489-96. PMID:12054627<ref>PMID:12054627</ref>
1KFA is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with GA4 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KFA OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Crystal structure of the liganded anti-gibberellin A(4) antibody 4-B8(8)/E9 Fab fragment., Murata T, Fushinobu S, Nakajima M, Asami O, Sassa T, Wakagi T, Yamaguchi I, Biochem Biophys Res Commun. 2002 Apr 26;293(1):489-96. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12054627 12054627]
</div>
[[Category: Homo sapiens]]
<div class="pdbe-citations 1kfa" style="background-color:#fffaf0;"></div>
[[Category: Protein complex]]
[[Category: Asami, O.]]
[[Category: Fushinobu, S.]]
[[Category: Murata, T.]]
[[Category: Nakajima, M.]]
[[Category: Sassa, T.]]
[[Category: Wakagi, T.]]
[[Category: Yamaguchi, I.]]
[[Category: GA4]]
[[Category: immunoglobuiln fold]]


''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:34:59 2007''
==See Also==
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Asami O]]
[[Category: Fushinobu S]]
[[Category: Murata T]]
[[Category: Nakajima M]]
[[Category: Sassa T]]
[[Category: Wakagi T]]
[[Category: Yamaguchi I]]
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