1m71: Difference between revisions

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-[[Image:1m71.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1m71", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1m71|  PDB=1m71  |  SCENE=  }}
-'''Crystal structure of a Monoclonal Fab Specific for Shigella Flexneri Y lipopolysaccharide'''
+==Crystal structure of a Monoclonal Fab Specific for Shigella Flexneri Y lipopolysaccharide==
+<StructureSection load='1m71' size='340' side='right'caption='[[1m71]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1m71]] 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=1M71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M71 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]] 2.8&#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=1m71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m71 OCA], [https://pdbe.org/1m71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m71 RCSB], [https://www.ebi.ac.uk/pdbsum/1m71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m71 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HVM32_MOUSE HVM32_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/m7/1m71_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=1m71 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The antigenic recognition of Shigella flexneri O-polysaccharide, which consists of a repeating unit ABCD [--&gt;2)-alpha-L-Rhap-(1--&gt;2)-alpha-L-Rhap-(1--&gt;3)-alpha-L-Rhap-(1--&gt;3)-beta -D-GlcpNAc-(1--&gt;], by the monoclonal antibody SYA/J6 (IgG3, kappa) has been investigated by crystallographic analysis of the Fab domain and its two complexes with two antigen segments (a pentasaccharide Rha A-Rha B-Rha C-GlcNAc D-Rha A' and a modified trisaccharide Rha B-Rha C-GlcNAc D in which Rha C* is missing a C2-OH group). These complex structures, the first for a Fab specific for a periodic linear heteropolysaccharide, reveal a binding site groove (between the V(H) and V(L) domains) that makes polar and nonpolar contacts with all the sugar residues of the pentasaccharide. Both main-chain and side-chain atoms of the Fab are used in ligand binding. The charged side chain of Glu H50 of CDR H2 forms crucial hydrogen bonds to GlcNAc of the oligosaccharides. The modified trisaccharide is more buried and fits more snugly than the pentasaccharide. It also makes as many contacts (approximately 75) with the Fab as the pentasaccharide, including the same number of hydrogen bonds (eight, with four being identical). It is further engaged in more hydrophobic interactions than the pentasaccharide. These three features favorable to trisaccharide binding are consistent with the observation of a tighter complex with the trisaccharide than the pentasaccharide. Thermodynamic data demonstrate that the native tri- to pentasaccharides have free energies of binding in the range of 6.8-7.4 kcal mol(-1), and all but one of the hydrogen bonds to individual hydroxyl groups provide no more than approximately 0.7 kcal mol(-1). They further indicate that hydrophobic interactions make significant contributions to binding and, as the native epitope becomes larger across the tri-, tetra-, pentasaccharide series, entropy contributions to the free energy become dominant.
-==Overview==
+Molecular recognition of oligosaccharide epitopes by a monoclonal Fab specific for Shigella flexneri Y lipopolysaccharide: X-ray structures and thermodynamics.,Vyas NK, Vyas MN, Chervenak MC, Johnson MA, Pinto BM, Bundle DR, Quiocho FA Biochemistry. 2002 Nov 19;41(46):13575-86. PMID:12427018<ref>PMID:12427018</ref>
-The antigenic recognition of Shigella flexneri O-polysaccharide, which consists of a repeating unit ABCD [--&gt;2)-alpha-L-Rhap-(1--&gt;2)-alpha-L-Rhap-(1--&gt;3)-alpha-L-Rhap-(1--&gt;3)-beta -D-GlcpNAc-(1--&gt;], by the monoclonal antibody SYA/J6 (IgG3, kappa) has been investigated by crystallographic analysis of the Fab domain and its two complexes with two antigen segments (a pentasaccharide Rha A-Rha B-Rha C-GlcNAc D-Rha A' and a modified trisaccharide Rha B-Rha C-GlcNAc D in which Rha C* is missing a C2-OH group). These complex structures, the first for a Fab specific for a periodic linear heteropolysaccharide, reveal a binding site groove (between the V(H) and V(L) domains) that makes polar and nonpolar contacts with all the sugar residues of the pentasaccharide. Both main-chain and side-chain atoms of the Fab are used in ligand binding. The charged side chain of Glu H50 of CDR H2 forms crucial hydrogen bonds to GlcNAc of the oligosaccharides. The modified trisaccharide is more buried and fits more snugly than the pentasaccharide. It also makes as many contacts (approximately 75) with the Fab as the pentasaccharide, including the same number of hydrogen bonds (eight, with four being identical). It is further engaged in more hydrophobic interactions than the pentasaccharide. These three features favorable to trisaccharide binding are consistent with the observation of a tighter complex with the trisaccharide than the pentasaccharide. Thermodynamic data demonstrate that the native tri- to pentasaccharides have free energies of binding in the range of 6.8-7.4 kcal mol(-1), and all but one of the hydrogen bonds to individual hydroxyl groups provide no more than approximately 0.7 kcal mol(-1). They further indicate that hydrophobic interactions make significant contributions to binding and, as the native epitope becomes larger across the tri-, tetra-, pentasaccharide series, entropy contributions to the free energy become dominant.
-==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=1M71 OCA].
+</div>
+<div class="pdbe-citations 1m71" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Molecular recognition of oligosaccharide epitopes by a monoclonal Fab specific for Shigella flexneri Y lipopolysaccharide: X-ray structures and thermodynamics., Vyas NK, Vyas MN, Chervenak MC, Johnson MA, Pinto BM, Bundle DR, Quiocho FA, Biochemistry. 2002 Nov 19;41(46):13575-86. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12427018 12427018]
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-[[Category: Bundle, D R.]]
+== References ==
-[[Category: Chervenak, M C.]]
+<references/>
-[[Category: Johnson, M A.]]
+__TOC__
-[[Category: Pinto, B M.]]
+</StructureSection>
-[[Category: Quiocho, F A.]]
+[[Category: Large Structures]]
-[[Category: Vyas, M N.]]
+[[Category: Mus musculus]]
-[[Category: Vyas, N K.]]
+[[Category: Bundle DR]]
-[[Category: Anti-carbohydrate antibody]]
+[[Category: Chervenak MC]]
-[[Category: Fab-carbohydrate interaction]]
+[[Category: Johnson MA]]
-[[Category: Shigella o-antigen]]
+[[Category: Pinto BM]]
-[[Category: X-ray diffracrion]]
+[[Category: Quiocho FA]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 00:42:52 2008''
+[[Category: Vyas MN]]
+[[Category: Vyas NK]]