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| | ==Crystal structure of anti-polysialic acid antibody single chain Fv fragment (mAb735) complexed with octasialic acid== | | ==Crystal structure of anti-polysialic acid antibody single chain Fv fragment (mAb735) complexed with octasialic acid== |
| - | <StructureSection load='3wbd' size='340' side='right' caption='[[3wbd]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='3wbd' size='340' side='right'caption='[[3wbd]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wbd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WBD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WBD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wbd]] 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=3WBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WBD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=SIA:O-SIALIC+ACID'>SIA</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1plg|1plg]]</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=3wbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wbd OCA], [https://pdbe.org/3wbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wbd RCSB], [https://www.ebi.ac.uk/pdbsum/3wbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wbd ProSAT]</span></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=3wbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wbd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wbd RCSB], [http://www.ebi.ac.uk/pdbsum/3wbd PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3wbd" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Synthetic construct sequences]] | + | [[Category: Large Structures]] |
| - | [[Category: Hanashima, S]] | + | [[Category: Mus musculus]] |
| - | [[Category: Ikeda, A]] | + | [[Category: Hanashima S]] |
| - | [[Category: Kitajima, K]] | + | [[Category: Ikeda A]] |
| - | [[Category: Nagae, M]] | + | [[Category: Kitajima K]] |
| - | [[Category: Sato, C]] | + | [[Category: Nagae M]] |
| - | [[Category: Yamaguchi, Y]] | + | [[Category: Sato C]] |
| - | [[Category: Alpha2-8 linked polysialic acid]]
| + | [[Category: Yamaguchi Y]] |
| - | [[Category: Anti-polysialic acid]]
| + | |
| - | [[Category: Beta-sandwich]]
| + | |
| - | [[Category: Immune system]]
| + | |
| - | [[Category: Immunoglobulin fold]]
| + | |
| - | [[Category: Single chain fv fragment]]
| + | |
| Structural highlights
Publication Abstract from PubMed
Polysialic acid is a linear homopolymer of alpha2-8-linked sialic acids attached mainly onto glycoproteins. Cell surface polysialic acid plays roles in cell adhesion and differentiation events in a manner that is often dependent on the degree of polymerization (DP). Anti-oligo/polysialic acid antibodies have DP-dependent antigenic specificity, and such antibodies are widely utilized in biological studies for detecting and distinguishing between different oligo/polysialic acids. A murine monoclonal antibody mAb735 has a unique preference for longer polymers of polysialic acid (DP >10), yet the mechanism of recognition at the atomic level remains unclear. Here, we report the crystal structure of mAb735 single chain variable fragment (scFv735) in complex with octasialic acid at 1.8 A resolution. In the asymmetric unit, two scFv735 molecules associate with one octasialic acid. In both complexes of the unit, all the complementarity-determining regions except for L3 interact with three consecutive sialic acid residues out of the eight. A striking feature of the complex is that 11 ordered water molecules bridge the gap between antibody and ligand, whereas the direct antibody-ligand interaction is less extensive. The dihedral angles of the trisialic acid unit directly interacting with scFv735 are not uniform, indicating that mAb735 does not strictly favor the previously proposed helical conformation. Importantly, both reducing and nonreducing ends of the bound ligand are completely exposed to solvent. We suggest that mAb735 gains its apparent high affinity for a longer polysialic acid chain by recognizing every three sialic acid units in a paired manner.
Crystal structure of anti-polysialic acid antibody single chain Fv fragment complexed with octasialic acid: insight into the binding preference for polysialic acid.,Nagae M, Ikeda A, Hane M, Hanashima S, Kitajima K, Sato C, Yamaguchi Y J Biol Chem. 2013 Nov 22;288(47):33784-96. doi: 10.1074/jbc.M113.496224. Epub, 2013 Oct 7. PMID:24100042[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Nagae M, Ikeda A, Hane M, Hanashima S, Kitajima K, Sato C, Yamaguchi Y. Crystal structure of anti-polysialic acid antibody single chain Fv fragment complexed with octasialic acid: insight into the binding preference for polysialic acid. J Biol Chem. 2013 Nov 22;288(47):33784-96. doi: 10.1074/jbc.M113.496224. Epub, 2013 Oct 7. PMID:24100042 doi:http://dx.doi.org/10.1074/jbc.M113.496224
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