2q76: Difference between revisions

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[[Image:2q76.jpg|left|200px]]
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{{STRUCTURE_2q76|  PDB=2q76  |  SCENE=  }}
'''Mouse anti-hen egg white lysozyme antibody F10.6.6 Fab fragment'''


==Mouse anti-hen egg white lysozyme antibody F10.6.6 Fab fragment==
<StructureSection load='2q76' size='340' side='right'caption='[[2q76]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2q76]] 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=2Q76 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q76 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&#8491;</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=2q76 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q76 OCA], [https://pdbe.org/2q76 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q76 RCSB], [https://www.ebi.ac.uk/pdbsum/2q76 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q76 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/q7/2q76_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=2q76 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The somatic mutations accumulated in variable and framework regions of antibodies produce structural changes that increase the affinity towards the antigen. This implies conformational and non covalent bonding changes at the paratope, as well as possible quaternary structure changes and rearrangements at the V(H)-V(L) interface. The consequences of the affinity maturation on the stability of the Fv domain were studied in a system composed of two closely related antibodies, F10.6.6 and D44.1, which recognize the same hen egg-white lysozyme (HEL) epitope. The mAb F10.6.6 has an affinity constant 700 times higher than D44.1, due to a higher surface complementarity to HEL. The structure of the free form of the Fab F10.6.6 presented here allows a comparative study of the conformational changes produced upon binding to antigen. By means of structural comparison, kinetics and thermodynamics of binding and stability studies on Fab and Fv fragments of both antibodies, we have determined that the affinity maturation process of anti-protein antibodies affects the shape of the combining site and the secondary structure content of the variable domain, stabilizes the V(H)-V(L) interaction, and consequently produces an increase of the Fv domain stability, improving the binding to antigen.


==Overview==
Affinity maturation increases the stability and plasticity of the Fv domain of anti-protein antibodies.,Acierno JP, Braden BC, Klinke S, Goldbaum FA, Cauerhff A J Mol Biol. 2007 Nov 16;374(1):130-46. Epub 2007 Sep 11. PMID:17916365<ref>PMID:17916365</ref>
The somatic mutations accumulated in variable and framework regions of antibodies produce structural changes that increase the affinity towards the antigen. This implies conformational and non covalent bonding changes at the paratope, as well as possible quaternary structure changes and rearrangements at the V(H)-V(L) interface. The consequences of the affinity maturation on the stability of the Fv domain were studied in a system composed of two closely related antibodies, F10.6.6 and D44.1, which recognize the same hen egg-white lysozyme (HEL) epitope. The mAb F10.6.6 has an affinity constant 700 times higher than D44.1, due to a higher surface complementarity to HEL. The structure of the free form of the Fab F10.6.6 presented here allows a comparative study of the conformational changes produced upon binding to antigen. By means of structural comparison, kinetics and thermodynamics of binding and stability studies on Fab and Fv fragments of both antibodies, we have determined that the affinity maturation process of anti-protein antibodies affects the shape of the combining site and the secondary structure content of the variable domain, stabilizes the V(H)-V(L) interaction, and consequently produces an increase of the Fv domain stability, improving the binding to antigen.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q76 OCA].
</div>
<div class="pdbe-citations 2q76" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Affinity maturation increases the stability and plasticity of the Fv domain of anti-protein antibodies., Acierno JP, Braden BC, Klinke S, Goldbaum FA, Cauerhff A, J Mol Biol. 2007 Nov 16;374(1):130-46. Epub 2007 Sep 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17916365 17916365]
*[[Antibody 3D structures|Antibody 3D structures]]
[[Category: Acierno, J P.]]
*[[Sandbox 20009|Sandbox 20009]]
[[Category: Braden, B C.]]
*[[3D structures of non-human antibody|3D structures of non-human antibody]]
[[Category: Cauerhff, A.]]
== References ==
[[Category: Goldbaum, F A.]]
<references/>
[[Category: Klinke, S.]]
__TOC__
[[Category: Affinity maturation]]
</StructureSection>
[[Category: Antibody]]
[[Category: Large Structures]]
[[Category: Fab fragment]]
[[Category: Mus musculus]]
[[Category: Immune system]]
[[Category: Acierno JP]]
[[Category: Lysozyme]]
[[Category: Braden BC]]
[[Category: Vh-vl interface.]]
[[Category: Cauerhff A]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 14:28:07 2008''
[[Category: Goldbaum FA]]
[[Category: Klinke S]]
Retrieved from "https://proteopedia.org/2q76"