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| | ==Crystal structure of S25-39 in complex with Kdo== | | ==Crystal structure of S25-39 in complex with Kdo== |
| - | <StructureSection load='3okd' size='340' side='right' caption='[[3okd]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='3okd' size='340' side='right'caption='[[3okd]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3okd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3OKD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3okd]] is a 2 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=3OKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OKD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3oke|3oke]], [[3okk|3okk]], [[3mhl|3mhl]], [[3mhm|3mhm]], [[3mhn|3mhn]], [[3mho|3mho]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3okd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okd OCA], [http://pdbe.org/3okd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3okd RCSB], [http://www.ebi.ac.uk/pdbsum/3okd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3okd ProSAT]</span></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=3okd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okd OCA], [https://pdbe.org/3okd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3okd RCSB], [https://www.ebi.ac.uk/pdbsum/3okd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3okd ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | ==See Also== | | ==See Also== |
| | *[[Antibody 3D structures|Antibody 3D structures]] | | *[[Antibody 3D structures|Antibody 3D structures]] |
| | + | *[[3D structures of non-human antibody|3D structures of non-human antibody]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Mus musculus]] | | [[Category: Mus musculus]] |
| - | [[Category: Blackler, R J]] | + | [[Category: Blackler RJ]] |
| - | [[Category: Evans, S V]] | + | [[Category: Evans SV]] |
| - | [[Category: Antibody]]
| + | |
| - | [[Category: Carbohydrate]]
| + | |
| - | [[Category: Fab]]
| + | |
| - | [[Category: Igg]]
| + | |
| - | [[Category: Immune system]]
| + | |
| Structural highlights
Publication Abstract from PubMed
The crystal structures of the antigen-binding fragment of the murine monoclonal antibody (mAb) S25-39 in the presence of several antigens representing chlamydial lipopolysaccharide (LPS) epitopes based on the bacterial sugar 3-deoxy-alpha-d-manno-oct-2-ulosonic acid (Kdo) have been determined at resolutions from 2.4 to 1.8 A. The antigen-binding site of this antibody differs from the well-characterized antibody S25-2 by a single mutation away from the germline of asparagine H53 to lysine, yet this one mutation results in a significant increase in avidity across a range of antigens. A comparison of the two antibody structures reveals that the mutated Lys H53 forms additional hydrogen bonds and/or charged-residue interactions with the second Kdo residue of every antigen having two or more carbohydrate residues. Significantly, the NH53K mutation results from a single nucleotide substitution in the germline sequence common among a panel of antibodies raised against glycoconjugates containing carbohydrate epitopes of chlamydial LPS. Like S25-2, S25-39 displays significant induced fit of complementarity determining region (CDR) H3 upon antigen binding, with the unliganded structure possessing a conformation distinct from those reported earlier for S25-2. The four different observed conformations for CDR H3 suggest that this CDR has evolved to exploit the recognition potential of a flexible loop while minimizing the associated entropic penalties of binding by adopting a limited number of ordered conformations in the unliganded state. These observations reveal strategies evolved to balance adaptability and specificity in the germline antibody response to carbohydrate antigens.
A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity.,Blackler RJ, Muller-Loennies S, Brooks CL, Evans DW, Brade L, Kosma P, Brade H, Evans SV Biochemistry. 2011 Apr 1. PMID:21405106[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Blackler RJ, Muller-Loennies S, Brooks CL, Evans DW, Brade L, Kosma P, Brade H, Evans SV. A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity. Biochemistry. 2011 Apr 1. PMID:21405106 doi:10.1021/bi101886v
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