1q9l

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(New page: 200px<br /> <applet load="1q9l" size="450" color="white" frame="true" align="right" spinBox="true" caption="1q9l, resolution 2.28&Aring;" /> '''S25-2 Fab Unligande...)
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[[Image:1q9l.gif|left|200px]]<br />
 
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<applet load="1q9l" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1q9l, resolution 2.28&Aring;" />
 
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'''S25-2 Fab Unliganded 2'''<br />
 
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==Overview==
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==S25-2 Fab Unliganded 2==
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High-resolution structures reveal how a germline antibody can recognize a, range of clinically relevant carbohydrate epitopes. The germline response, to a carbohydrate immunogen can be critical to survivability, with, selection for antibody gene segments that both confer protection against, common pathogens and retain the flexibility to adapt to new disease, organisms. We show here that antibody S25-2 binds several distinct, inner-core epitopes of bacterial lipopolysaccharides (LPSs) by linking an, inherited monosaccharide residue binding site with a subset of, complementarity-determining regions (CDRs) of limited flexibility, positioned to recognize the remainder of an array of different epitopes., This strategy allows germline antibodies to adapt to different epitopes, while minimizing entropic penalties associated with the immobilization of, labile CDRs upon binding of antigen, and provides insight into the link, between the genetic origin of individual CDRs and their respective roles, in antigen recognition.
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<StructureSection load='1q9l' size='340' side='right'caption='[[1q9l]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1q9l]] 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=1Q9L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q9L 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]] 2.28&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1q9l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q9l OCA], [https://pdbe.org/1q9l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q9l RCSB], [https://www.ebi.ac.uk/pdbsum/1q9l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q9l 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/q9/1q9l_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=1q9l 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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High-resolution structures reveal how a germline antibody can recognize a range of clinically relevant carbohydrate epitopes. The germline response to a carbohydrate immunogen can be critical to survivability, with selection for antibody gene segments that both confer protection against common pathogens and retain the flexibility to adapt to new disease organisms. We show here that antibody S25-2 binds several distinct inner-core epitopes of bacterial lipopolysaccharides (LPSs) by linking an inherited monosaccharide residue binding site with a subset of complementarity-determining regions (CDRs) of limited flexibility positioned to recognize the remainder of an array of different epitopes. This strategy allows germline antibodies to adapt to different epitopes while minimizing entropic penalties associated with the immobilization of labile CDRs upon binding of antigen, and provides insight into the link between the genetic origin of individual CDRs and their respective roles in antigen recognition.
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==About this Structure==
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Germline antibody recognition of distinct carbohydrate epitopes.,Nguyen HP, Seto NO, MacKenzie CR, Brade L, Kosma P, Brade H, Evans SV Nat Struct Biol. 2003 Dec;10(12):1019-25. Epub 2003 Nov 16. PMID:14625588<ref>PMID:14625588</ref>
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1Q9L is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with ZN and MG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Q9L 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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Germline antibody recognition of distinct carbohydrate epitopes., Nguyen HP, Seto NO, MacKenzie CR, Brade L, Kosma P, Brade H, Evans SV, Nat Struct Biol. 2003 Dec;10(12):1019-25. Epub 2003 Nov 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14625588 14625588]
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</div>
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[[Category: Mus musculus]]
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<div class="pdbe-citations 1q9l" style="background-color:#fffaf0;"></div>
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[[Category: Protein complex]]
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[[Category: Brade, H.]]
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[[Category: Brade, L.]]
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[[Category: Evans, S.V.]]
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[[Category: Kosma, P.]]
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[[Category: MacKenzie, C.R.]]
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[[Category: Nguyen, H.P.]]
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[[Category: Seto, N.O.]]
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[[Category: MG]]
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[[Category: ZN]]
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[[Category: anti-carbohydrate]]
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[[Category: anti-lps]]
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[[Category: antibody]]
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[[Category: antigen-binding fragment]]
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[[Category: fab]]
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[[Category: immunoglobulin]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:40:04 2007''
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==See Also==
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*[[Antibody 3D structures|Antibody 3D structures]]
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*[[Sandbox 20009|Sandbox 20009]]
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
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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: Brade H]]
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[[Category: Brade L]]
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[[Category: Evans SV]]
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[[Category: Kosma P]]
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[[Category: MacKenzie CR]]
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[[Category: Nguyen HP]]
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[[Category: Seto NO]]

Current revision

S25-2 Fab Unliganded 2

PDB ID 1q9l

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