3phq: Difference between revisions

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-[[Image:3phq.jpg|left|200px]]
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+==Crystal structure of S64-4 in complex with KDO==
-The line below this paragraph, containing "STRUCTURE_3phq", creates the "Structure Box" on the page.
+<StructureSection load='3phq' size='340' side='right'caption='[[3phq]], [[Resolution|resolution]] 2.00&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'>[[3phq]] 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=3PHQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PHQ 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]] 2&#8491;</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></td></tr>
-{{STRUCTURE_3phq|  PDB=3phq  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3phq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3phq OCA], [https://pdbe.org/3phq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3phq RCSB], [https://www.ebi.ac.uk/pdbsum/3phq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3phq ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of the antigen-binding fragment from the monoclonal antibody S64-4 in complex with a pentasaccharide bisphosphate fragment from chlamydial lipopolysaccharide has been determined by x-ray diffraction to 2.6 A resolution. Like the well-characterized antibody S25-2, S64-4 displays a pocket formed by the residues of germline sequence corresponding to the heavy and light chain V genes that binds the terminal Kdo residue of the antigen; however, while S64-4 shares the same heavy chain V gene as S25-2 it has a different light chain V gene. The new V(L) gene codes for a combining site that displays greater affinity, different specificity, and allows a novel antigen conformation that brings a greater number of antigen residues into the combining site than possible in S25-2. Further, while antibodies in the S25-2 family use CDR H3 to discriminate among antigens, S64-4 achieves its specificity via the new light chain V gene and resulting change in antigen conformation. These structures reveal an intriguing parallel strategy where two different combinations of germline-coded V genes can act as starting points for the generation of germline antibodies against chlamydial antigens, and shows how anti-carbohydrate antibodies can exploit the conformational flexibility of this class of antigens to achieve high affinity and specificity independently of CDR H3.
-===Crystal structure of S64-4 in complex with KDO===
+Structural insights into parallel strategies for germline antibody recognition of LPS from Chlamydia.,Evans DW, Muller-Loennies S, Brooks CL, Brade L, Kosma P, Brade H, Evans SV Glycobiology. 2011 May 4. PMID:21543444<ref>PMID:21543444</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3phq" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21543444}}, adds the Publication Abstract to the page
+*[[Antibody 3D structures|Antibody 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21543444 is the PubMed ID number.
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
--->
+== References ==
-{{ABSTRACT_PUBMED_21543444}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-[[3phq]] 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=3PHQ OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:021543444</ref><references group="xtra"/>
 [[Category: Mus musculus]]
-[[Category: Evans, D W.]]
+[[Category: Evans DW]]
-[[Category: Evans, S V.]]
+[[Category: Evans SV]]