1xf2: Difference between revisions

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-{{Seed}}
-[[Image:1xf2.png|left|200px]]
-<!--
+==Structure of Fab DNA-1 complexed with dT3==
-The line below this paragraph, containing "STRUCTURE_1xf2", creates the "Structure Box" on the page.
+<StructureSection load='1xf2' size='340' side='right'caption='[[1xf2]], [[Resolution|resolution]] 2.30&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'>[[1xf2]] is a 5 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=1XF2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XF2 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1xf2|  PDB=1xf2  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xf2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xf2 OCA], [https://pdbe.org/1xf2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xf2 RCSB], [https://www.ebi.ac.uk/pdbsum/1xf2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xf2 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/xf/1xf2_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=1xf2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Anti-DNA antibodies play important roles in the pathogenesis of autoimmune diseases. They also represent a unique and relatively unexplored class of DNA-binding protein. Here, we present a study of conformational changes induced by DNA binding to an anti-ssDNA Fab known as DNA-1. Three crystal structures are reported: a complex of DNA-1 bound to dT3, and two structures of the ligand-free Fab. One of the ligand-free structures was determined from crystals exhibiting perfect hemihedral twinning, and the details of structure determination are provided. Unexpectedly, five residues (H97-H100A) in the apex of heavy chain complementarity-determining region 3 (HCDR3) are disordered in both ligand-free structures. Ligand binding also caused a 2-4A shift of the backbone of Tyr L92 and ordering of the L92 side-chain. In contrast, these residues are highly ordered in the Fab/dT3 complex, where Tyr H100 and Tyr H100A form intimate stacking interactions with DNA bases, and L92 forms the 5' end of the binding site. The structures suggest that HCDR3 is very flexible and adopts multiple conformations in the ligand-free state. These results are discussed in terms of induced fit and pre-existing equilibrium theories of ligand binding. Our results allow new interpretations of existing thermodynamic and mutagenesis data in terms of conformational entropy and the volume of conformational space accessible to HCDR3 in the ligand-free state. In the context of autoimmune disease, plasticity of the ligand-free antibody could provide a mechanism by which anti-DNA antibodies bind diverse host ligands, and thereby contribute to pathogenicity.
-===Structure of Fab DNA-1 complexed with dT3===
+Evidence for structural plasticity of heavy chain complementarity-determining region 3 in antibody-ssDNA recognition.,Schuermann JP, Prewitt SP, Davies C, Deutscher SL, Tanner JJ J Mol Biol. 2005 Apr 15;347(5):965-78. PMID:15784256<ref>PMID:15784256</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1xf2" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15784256}}, adds the Publication Abstract to the page
+*[[Antibody 3D structures|Antibody 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15784256 is the PubMed ID number.
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
--->
+== References ==
-{{ABSTRACT_PUBMED_15784256}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-XF2 is a 5 chains 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=1XF2 OCA].
+[[Category: Large Structures]]
-==Reference==
-<ref group="xtra">PMID:15784256</ref><references group="xtra"/>
 [[Category: Mus musculus]]
-[[Category: Deutscher, S L.]]
+[[Category: Deutscher SL]]
-[[Category: Prewitt, S P.]]
+[[Category: Prewitt SP]]
-[[Category: Schuermann, J P.]]
+[[Category: Schuermann JP]]
-[[Category: Tanner, J J.]]
+[[Category: Tanner JJ]]
-[[Category: Anti-dna]]
-[[Category: Anti-ssdna]]
-[[Category: Antibody]]
-[[Category: Autoantibody]]
-[[Category: Fab]]
-[[Category: Immunoglobulin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 06:03:30 2009''