This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2vlm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:39, 30 March 2022) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2vlm.png|left|200px]]
 
-
<!--
+
==The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are Programmed by its Vbeta Domain==
-
The line below this paragraph, containing "STRUCTURE_2vlm", creates the "Structure Box" on the page.
+
<StructureSection load='2vlm' size='340' side='right'caption='[[2vlm]], [[Resolution|resolution]] 1.98&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'>[[2vlm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. 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>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2vlj|2vlj]], [[2vlk|2vlk]], [[2vlr|2vlr]]</div></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=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>
-
{{STRUCTURE_2vlm| PDB=2vlm | SCENE= }}
+
</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/vl/2vlm_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_18275829}}, 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 18275829 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_18275829}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Human]]
-
2VLM 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].
+
[[Category: Large Structures]]
-
 
+
[[Category: Bell, J]]
-
==Reference==
+
[[Category: Ishizuka, J]]
-
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: Jones, Y]]
-
[[Category: Homo sapiens]]
+
[[Category: McMichael, A]]
-
[[Category: Single protein]]
+
[[Category: Merwe, A Van der]]
-
[[Category: Bell, J.]]
+
[[Category: Stewart-Jones, G]]
-
[[Category: Ishizuka, J.]]
+
-
[[Category: Jones, Y.]]
+
-
[[Category: Mcmichael, A.]]
+
-
[[Category: Merwe, A Van Der.]]
+
-
[[Category: Stewart-Jones, G.]]
+
[[Category: Complex]]
[[Category: Complex]]
[[Category: Flu]]
[[Category: Flu]]
[[Category: Host-virus interaction]]
[[Category: Host-virus interaction]]
[[Category: Immune response]]
[[Category: Immune response]]
-
[[Category: Immune system/receptor/complex]]
+
[[Category: Immune system]]
 +
[[Category: Immune system-receptor-complex]]
[[Category: Immunodominance]]
[[Category: Immunodominance]]
[[Category: Immunoglobulin domain]]
[[Category: Immunoglobulin domain]]
Line 42: Line 52:
[[Category: Mhc]]
[[Category: Mhc]]
[[Category: Mhc i]]
[[Category: Mhc i]]
-
[[Category: Peptide]]
 
-
[[Category: Polymorphism]]
 
[[Category: Receptor]]
[[Category: Receptor]]
[[Category: T-cell]]
[[Category: T-cell]]
[[Category: Tcr]]
[[Category: Tcr]]
- 
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:54:15 2008''
 

Current revision

The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are Programmed by its Vbeta Domain

PDB ID 2vlm

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vlm"
Personal tools