1d9k: Difference between revisions

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-{{Seed}}
-[[Image:1d9k.png|left|200px]]
-<!--
+==CRYSTAL STRUCTURE OF COMPLEX BETWEEN D10 TCR AND PMHC I-AK/CA==
-The line below this paragraph, containing "STRUCTURE_1d9k", creates the "Structure Box" on the page.
+<StructureSection load='1d9k' size='340' side='right'caption='[[1d9k]], [[Resolution|resolution]] 3.20&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'>[[1d9k]] is a 10 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=1D9K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D9K 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]] 3.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>
-{{STRUCTURE_1d9k|  PDB=1d9k  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d9k OCA], [https://pdbe.org/1d9k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d9k RCSB], [https://www.ebi.ac.uk/pdbsum/1d9k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d9k ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TVA2_MOUSE TVA2_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/d9/1d9k_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=1d9k ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of a complex involving the D10 T cell receptor (TCR), 16-residue foreign peptide antigen, and the I-Ak self major histocompatibility complex (MHC) class II molecule is reported at 3.2 angstrom resolution. The D10 TCR is oriented in an orthogonal mode relative to its peptide-MHC (pMHC) ligand, necessitated by the amino-terminal extension of peptide residues projecting from the MHC class II antigen-binding groove as part of a mini beta sheet. Consequently, the disposition of D10 complementarity-determining region loops is altered relative to that of most pMHCI-specific TCRs; the latter TCRs assume a diagonal orientation, although with substantial variability. Peptide recognition, which involves P-1 to P8 residues, is dominated by the Valpha domain, which also binds to the class II MHC beta1 helix. That docking is limited to one segment of MHC-bound peptide offers an explanation for epitope recognition and altered peptide ligand effects, suggests a structural basis for alloreactivity, and illustrates how bacterial superantigens can span the TCR-pMHCII surface.
-===CRYSTAL STRUCTURE OF COMPLEX BETWEEN D10 TCR AND PMHC I-AK/CA===
+The crystal structure of a T cell receptor in complex with peptide and MHC class II.,Reinherz EL, Tan K, Tang L, Kern P, Liu J, Xiong Y, Hussey RE, Smolyar A, Hare B, Zhang R, Joachimiak A, Chang HC, Wagner G, Wang J Science. 1999 Dec 3;286(5446):1913-21. PMID:10583947<ref>PMID:10583947</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1d9k" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10583947}}, adds the Publication Abstract to the page
+*[[T-cell receptor 3D structures|T-cell receptor 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10583947 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10583947}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-D9K is a 10 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=1D9K OCA].
-==Reference==
-<ref group="xtra">PMID:10583947</ref><references group="xtra"/>
 [[Category: Mus musculus]]
-[[Category: Chang, H C.]]
+[[Category: Chang H-C]]
-[[Category: Hare, B.]]
+[[Category: Hare B]]
-[[Category: Hussey, R E.]]
+[[Category: Hussey RE]]
-[[Category: Joachimiak, A.]]
+[[Category: Joachimiak A]]
-[[Category: Kern, P.]]
+[[Category: Kern P]]
-[[Category: Liu, J H.]]
+[[Category: Liu J-H]]
-[[Category: Reinherz, E L.]]
+[[Category: Reinherz EL]]
-[[Category: Smolyar, A.]]
+[[Category: Smolyar A]]
-[[Category: Tan, K.]]
+[[Category: Tan K]]
-[[Category: Tang, L.]]
+[[Category: Tang L]]
-[[Category: Wagner, G.]]
+[[Category: Wagner G]]
-[[Category: Wang, J-H.]]
+[[Category: Wang J-H]]
-[[Category: Xiong, Y.]]
+[[Category: Xiong Y]]
-[[Category: Zhang, R.]]
+[[Category: Zhang R]]
-[[Category: D10]]
-[[Category: I-ak]]
-[[Category: Mhc class ii]]
-[[Category: T-cell receptor]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:52:53 2009''