2vlm: Difference between revisions

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-[[Image:2vlm.jpg|left|200px]]
- {{Structure
+==The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are Programmed by its Vbeta Domain==
-|PDB= 2vlm |SIZE=350|CAPTION= <scene name='initialview01'>2vlm</scene>, resolution 1.98&Aring;
+<StructureSection load='2vlm' size='340' side='right'caption='[[2vlm]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[2vlm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VLM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VLM FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98&#8491;</td></tr>
-|GENE=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vlm OCA], [https://pdbe.org/2vlm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vlm RCSB], [https://www.ebi.ac.uk/pdbsum/2vlm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vlm ProSAT]</span></td></tr>
-|DOMAIN=
+</table>
-|RELATEDENTRY=[[2vlj|2VLJ]], [[2vlk|2VLK]], [[2vlr|2VLR]]
+== Evolutionary Conservation ==
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vlm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vlm OCA], [http://www.ebi.ac.uk/pdbsum/2vlm PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2vlm RCSB]</span>
+[[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/vl/2vlm_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=2vlm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Immunodominant and public T cell receptor (TCR) usage is relatively common in many viral diseases yet surprising in the context of the large naive TCR repertoire. We examined the highly conserved Vbeta17:Valpha10.2 JM22 T cell response to the influenza matrix peptide (58-66)-HLA-A*0201 (HLA-A2-flu) through extensive kinetic, thermodynamic, and structural analyses. We found several conformational adjustments that accompany JM22-HLA-A2-flu binding and identified a binding "hotspot" within the Vbeta domain of the TCR. Within this hotspot, key germline-encoded CDR1 and CDR2 loop residues and a crucial but commonly coded residue in the hypervariable region of CDR3 provide the basis for the substantial bias in the selection of the germline-encoded Vbeta17 domain. The chances of having a substantial number of T cells in the naive repertoire that have HLA-A2-flu-specific Vbeta17 receptors may consequently be relatively high, thus explaining the immunodominant usage of this clonotype.
-'''THE STRUCTURAL DYNAMICS AND ENERGETICS OF AN IMMUNODOMINANT T-CELL RECEPTOR ARE PROGRAMMED BY ITS VBETA DOMAIN'''
+The structural dynamics and energetics of an immunodominant T cell receptor are programmed by its Vbeta domain.,Ishizuka J, Stewart-Jones GB, van der Merwe A, Bell JI, McMichael AJ, Jones EY Immunity. 2008 Feb;28(2):171-82. PMID:18275829<ref>PMID:18275829</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vlm" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Immunodominant and public T cell receptor (TCR) usage is relatively common in many viral diseases yet surprising in the context of the large naive TCR repertoire. We examined the highly conserved Vbeta17:Valpha10.2 JM22 T cell response to the influenza matrix peptide (58-66)-HLA-A( *)0201 (HLA-A2-flu) through extensive kinetic, thermodynamic, and structural analyses. We found several conformational adjustments that accompany JM22-HLA-A2-flu binding and identified a binding "hotspot" within the Vbeta domain of the TCR. Within this hotspot, key germline-encoded CDR1 and CDR2 loop residues and a crucial but commonly coded residue in the hypervariable region of CDR3 provide the basis for the substantial bias in the selection of the germline-encoded Vbeta17 domain. The chances of having a substantial number of T cells in the naive repertoire that have HLA-A2-flu-specific Vbeta17 receptors may consequently be relatively high, thus explaining the immunodominant usage of this clonotype.
+*[[T-cell receptor 3D structures|T-cell receptor 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-VLM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VLM OCA].
+__TOC__
+</StructureSection>
-==Reference==
-The structural dynamics and energetics of an immunodominant T cell receptor are programmed by its Vbeta domain., Ishizuka J, Stewart-Jones GB, van der Merwe A, Bell JI, McMichael AJ, Jones EY, Immunity. 2008 Feb;28(2):171-82. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18275829 18275829]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bell, J.]]
+[[Category: Bell J]]
-[[Category: Ishizuka, J.]]
+[[Category: Ishizuka J]]
-[[Category: Jones, Y.]]
+[[Category: Jones Y]]
-[[Category: Mcmichael, A.]]
+[[Category: McMichael A]]
-[[Category: Merwe, A Van Der.]]
+[[Category: Stewart-Jones G]]
-[[Category: Stewart-Jones, G.]]
+[[Category: Van der Merwe A]]
-[[Category: complex]]
-[[Category: flu]]
-[[Category: host-virus interaction]]
-[[Category: immune response]]
-[[Category: immune system/receptor/complex]]
-[[Category: immunodominance]]
-[[Category: immunoglobulin domain]]
-[[Category: membrane]]
-[[Category: mhc]]
-[[Category: mhc i]]
-[[Category: peptide]]
-[[Category: polymorphism]]
-[[Category: receptor]]
-[[Category: t-cell]]
-[[Category: tcr]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:13:31 2008''