3bz4: Difference between revisions

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-{{Seed}}
-[[Image:3bz4.png|left|200px]]
-<!--
+==Crystal structure of Fab F22-4 in complex with a Shigella flexneri 2a O-Ag decasaccharide==
-The line below this paragraph, containing "STRUCTURE_3bz4", creates the "Structure Box" on the page.
+<StructureSection load='3bz4' size='340' side='right'caption='[[3bz4]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3bz4]] is a 8 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=3BZ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BZ4 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EAG:2-AMINOETHYL+2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSIDE'>EAG</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PD:PALLADIUM+ION'>PD</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene></td></tr>
-{{STRUCTURE_3bz4|  PDB=3bz4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bz4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bz4 OCA], [https://pdbe.org/3bz4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bz4 RCSB], [https://www.ebi.ac.uk/pdbsum/3bz4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bz4 ProSAT]</span></td></tr>
+</table>
+== 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/bz/3bz4_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=3bz4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The anti-LPS IgG mAb F22-4, raised against Shigella flexneri serotype 2a bacteria, protects against homologous, but not heterologous, challenge in an experimental animal model. We report the crystal structures of complexes formed between Fab F22-4 and two synthetic oligosaccharides, a decasaccharide and a pentadecasaccharide that were previously shown to be both immunogenic and antigenic mimics of the S. flexneri serotype 2a O-antigen. F22-4 binds to an epitope contained within two consecutive 2a serotype pentasaccharide repeat units (RU). Six sugar residues from a contiguous nine-residue segment make direct contacts with the antibody, including the nonreducing rhamnose and both branching glucosyl residues from the two RUs. The glucosyl residue, whose position of attachment to the tetrasaccharide backbone of the RU defines the serotype 2a O-antigen, is critical for recognition by F22-4. Although the complete decasaccharide is visible in the electron density maps, the last four pentadecasaccharide residues from the reducing end, which do not contact the antibody, could not be traced. Although considerable mobility in the free oligosaccharides can thus be expected, the conformational similarity between the individual RUs, both within and between the two complexes, suggests that short-range transient ordering to a helical conformation might occur in solution. Although the observed epitope includes the terminal nonreducing residue, binding to internal epitopes within the polysaccharide chain is not precluded. Our results have implications for vaccine development because they suggest that a minimum of two RUs of synthetic serotype 2a oligosaccharide is required for optimal mimicry of O-Ag epitopes.
-===Crystal structure of Fab F22-4 in complex with a Shigella flexneri 2a O-Ag decasaccharide===
+Structures of synthetic O-antigen fragments from serotype 2a Shigella flexneri in complex with a protective monoclonal antibody.,Vulliez-Le Normand B, Saul FA, Phalipon A, Belot F, Guerreiro C, Mulard LA, Bentley GA Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):9976-81. Epub 2008 Jul 10. PMID:18621718<ref>PMID:18621718</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3bz4" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18621718}}, adds the Publication Abstract to the page
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18621718 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18621718}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-BZ4 is a [[Protein complex]] structure of sequences 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=3BZ4 OCA].
-==Reference==
-Structures of synthetic O-antigen fragments from serotype 2a Shigella flexneri in complex with a protective monoclonal antibody., Vulliez-Le Normand B, Saul FA, Phalipon A, Belot F, Guerreiro C, Mulard LA, Bentley GA, Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):9976-81. Epub 2008 Jul 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18621718 18621718]
 [[Category: Mus musculus]]
-[[Category: Protein complex]]
+[[Category: Bentley GA]]
-[[Category: Bentley, G A.]]
+[[Category: Saul FA]]
-[[Category: Saul, F A.]]
+[[Category: Vulliez-le-Normand B]]
-[[Category: Vulliez-le-Normand, B.]]
-[[Category: Antibody complex]]
-[[Category: Immune system]]
-[[Category: Lp]]
-[[Category: O-antigen]]
-[[Category: Shigella flexneri]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug  6 09:59:39 2008''