2dqf: Difference between revisions

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-{{Seed}}
-[[Image:2dqf.png|left|200px]]
-<!--
+==Crystal structure of hyhel-10 FV mutant (y33ay53a) complexed with hen egg lysozyme==
-The line below this paragraph, containing "STRUCTURE_2dqf", creates the "Structure Box" on the page.
+<StructureSection load='2dqf' size='340' side='right'caption='[[2dqf]], [[Resolution|resolution]] 2.50&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'>[[2dqf]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DQF 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]] 2.5&#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=2dqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dqf OCA], [https://pdbe.org/2dqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dqf RCSB], [https://www.ebi.ac.uk/pdbsum/2dqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dqf ProSAT]</span></td></tr>
-{{STRUCTURE_2dqf|  PDB=2dqf  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q65ZI1_MOUSE Q65ZI1_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/dq/2dqf_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=2dqf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Tyrosine is an important amino acid in protein-protein interaction hot spots. In particular, many Tyr residues are located in the antigen-binding sites of antibodies and endow high affinity and high specificity to these antibodies. To investigate the role of interfacial Tyr residues in protein-protein interactions, we performed crystallographic studies and thermodynamic analyses of the interaction between hen egg lysozyme (HEL) and the anti-HEL antibody HyHEL-10 Fv fragment. HyHEL-10 has six Tyr residues in its antigen-binding site, which were systematically mutated to Phe and Ala using site-directed mutagenesis. The crystal structures revealed several critical roles for these Tyr residues in the interaction between HEL and HyHEL-10 as follows: 1) the aromatic ring of Tyr-50 in the light chain (LTyr-50) was important for the correct ternary structure of variable regions of the immunoglobulin light chain and heavy chain and of HEL; 2) deletion of the hydroxyl group of Tyr-50 in the heavy chain (HTyr-50) resulted in structural changes in the antigen-antibody interface; and 3) the side chains of HTyr-33 and HTyr-53 may help induce fitting of the antibody to the antigen. Hot spot Tyr residues may contribute to the high affinity and high specificity of the antigen-antibody interaction through a diverse set of structural and thermodynamic interactions.
-===Crystal structure of hyhel-10 FV mutant (y33ay53a) complexed with hen egg lysozyme===
+Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL.,Shiroishi M, Tsumoto K, Tanaka Y, Yokota A, Nakanishi T, Kondo H, Kumagai I J Biol Chem. 2007 Mar 2;282(9):6783-91. Epub 2006 Dec 12. PMID:17166830<ref>PMID:17166830</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2dqf" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17166830}}, adds the Publication Abstract to the page
+*[[Lysozyme 3D structures|Lysozyme 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17166830 is the PubMed ID number.
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_17166830}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-DQF is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQF OCA].
-==Reference==
-Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL., Shiroishi M, Tsumoto K, Tanaka Y, Yokota A, Nakanishi T, Kondo H, Kumagai I, J Biol Chem. 2007 Mar 2;282(9):6783-91. Epub 2006 Dec 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17166830 17166830]
 [[Category: Gallus gallus]]
-[[Category: Lysozyme]]
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Protein complex]]
+[[Category: Kondo H]]
-[[Category: Kondo, H.]]
+[[Category: Kumagai I]]
-[[Category: Kumagai, I.]]
+[[Category: Shiroishi M]]
-[[Category: Shiroishi, M.]]
+[[Category: Tsumoto K]]
-[[Category: Tsumoto, K.]]
-[[Category: Antigen-antibody complex]]
-[[Category: Immune system/hydrolase complex]]
-[[Category: Mutant]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 12:56:18 2008''