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1mfd

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(New page: 200px<br /> <applet load="1mfd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1mfd, resolution 2.1&Aring;" /> '''THE SOLUTION STRUCTU...)
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[[Image:1mfd.gif|left|200px]]<br />
 
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<applet load="1mfd" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1mfd, resolution 2.1&Aring;" />
 
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'''THE SOLUTION STRUCTURE OF A TRISACCHARIDE-ANTIBODY COMPLEX: COMPARISON OF NMR MEASUREMENTS WITH A CRYSTAL STRUCTURE'''<br />
 
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==Overview==
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==THE SOLUTION STRUCTURE OF A TRISACCHARIDE-ANTIBODY COMPLEX: COMPARISON OF NMR MEASUREMENTS WITH A CRYSTAL STRUCTURE==
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NMR and crystallography have been used to study antigen conformational, changes that occur in a trisaccharide-Fab complex in solution and in the, solid state. NOE buildup rates from transferred NOE experiments show that, the antigenic determinant of a Salmonella lipopolysaccharide, represented, by the trisaccharide methyl glycoside alpha-D-Galp(1--&gt;2, [alpha-D-Abep(1--&gt;3)]- alpha-D-Manp1--&gt;OMe (1), undergoes a, protein-induced conformational shift about the Gal--&gt;Man glycosidic, linkage when it is bound by a monoclonal antibody in aqueous solution. The, same trisaccharide was crystallized with Fab, and a solved structure at, 2.1-A resolution revealed that the conformation of the trisaccharide, ligand was similar to that seen in a dodesaccharide-Fab complex [Cygler et, al. (1991) Science 253, 442-445), where the Gal-Man linkage also, experienced a similar conformational shift. Distance constraints derived, from the TRNOE buildup curves are consistent with two bound trisaccharide, conformations, one of which correlates with the ligand conformation of the, crystalline Fab-trisaccharide complex. In this bound conformation, short, interatomic distances between Abe O-2 and Gal O-2 permit an, oligosaccharide intramolecular hydrogen bond. Despite its relatively low, energy, a preponderance of this conformer could not be detected in aqueous, or DMSO solutions of free trisaccharide by either 1H or 13C NMR, experiments. In DMSO, a different intramolecular hydrogen bond between Abe, O-2 and Man O-4 was observed due to a solvent-induced shift in the, conformational equilibria (relative to aqueous solution). Molecular, modeling of the trisaccharide in the binding site and as the free ligand, suggested that the protein imposes an induced fit on the antigen, primarily resulting in a shift of the Gal-Man phi torsional angle. This, reduces the interproton separation between Abe H-3 and Gal H-1 with a, marked increase in the intensity of the previously weak NOEs between the, protons of the noncovalently linked galactose and abequose residues. The, impact of the conformational shift on gross trisaccharide topology is, sufficiently small that binding modes inferred from functional group, replacements are not impaired.
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<StructureSection load='1mfd' size='340' side='right'caption='[[1mfd]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1mfd]] 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=1MFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MFD 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]] 2.1&#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=ABE:ABEQUOSE'>ABE</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=MMA:O1-METHYL-MANNOSE'>MMA</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=1mfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mfd OCA], [https://pdbe.org/1mfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mfd RCSB], [https://www.ebi.ac.uk/pdbsum/1mfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mfd 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/mf/1mfd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1mfd ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1MFD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MFD OCA].
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*[[Antibody 3D structures|Antibody 3D structures]]
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
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==Reference==
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__TOC__
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Solution structure of a trisaccharide-antibody complex: comparison of NMR measurements with a crystal structure., Bundle DR, Baumann H, Brisson JR, Gagne SM, Zdanov A, Cygler M, Biochemistry. 1994 May 3;33(17):5183-92. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8172893 8172893]
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</StructureSection>
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Cygler, M.]]
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[[Category: Mus musculus]]
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[[Category: Zdanov, A.]]
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[[Category: Cygler M]]
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[[Category: immunoglobulin]]
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[[Category: Zdanov A]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:36:33 2007''
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Current revision

THE SOLUTION STRUCTURE OF A TRISACCHARIDE-ANTIBODY COMPLEX: COMPARISON OF NMR MEASUREMENTS WITH A CRYSTAL STRUCTURE

PDB ID 1mfd

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