1t5x: Difference between revisions

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-{{Seed}}
-[[Image:1t5x.png|left|200px]]
-<!--
+==HLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR) and the superantigen SEC3-3B2==
-The line below this paragraph, containing "STRUCTURE_1t5x", creates the "Structure Box" on the page.
+<StructureSection load='1t5x' size='340' side='right'caption='[[1t5x]], [[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'>[[1t5x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens], [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] and [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T5X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T5X 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=1t5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t5x OCA], [https://pdbe.org/1t5x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t5x RCSB], [https://www.ebi.ac.uk/pdbsum/1t5x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t5x ProSAT]</span></td></tr>
-{{STRUCTURE_1t5x|  PDB=1t5x  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DRA_HUMAN DRA_HUMAN] Binds peptides derived from antigens that access the endocytic route of antigen presenting cells (APC) and presents them on the cell surface for recognition by the CD4 T-cells. The peptide binding cleft accommodates peptides of 10-30 residues. The peptides presented by MHC class II molecules are generated mostly by degradation of proteins that access the endocytic route, where they are processed by lysosomal proteases and other hydrolases. Exogenous antigens that have been endocytosed by the APC are thus readily available for presentation via MHC II molecules, and for this reason this antigen presentation pathway is usually referred to as exogenous. As membrane proteins on their way to degradation in lysosomes as part of their normal turn-over are also contained in the endosomal/lysosomal compartments, exogenous antigens must compete with those derived from endogenous components. Autophagy is also a source of endogenous peptides, autophagosomes constitutively fuse with MHC class II loading compartments. In addition to APCs, other cells of the gastrointestinal tract, such as epithelial cells, express MHC class II molecules and CD74 and act as APCs, which is an unusual trait of the GI tract. To produce a MHC class II molecule that presents an antigen, three MHC class II molecules (heterodimers of an alpha and a beta chain) associate with a CD74 trimer in the ER to form a heterononamer. Soon after the entry of this complex into the endosomal/lysosomal system where antigen processing occurs, CD74 undergoes a sequential degradation by various proteases, including CTSS and CTSL, leaving a small fragment termed CLIP (class-II-associated invariant chain peptide). The removal of CLIP is facilitated by HLA-DM via direct binding to the alpha-beta-CLIP complex so that CLIP is released. HLA-DM stabilizes MHC class II molecules until primary high affinity antigenic peptides are bound. The MHC II molecule bound to a peptide is then transported to the cell membrane surface. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO. Primary dendritic cells (DCs) also to express HLA-DO. Lysosomal miroenvironment has been implicated in the regulation of antigen loading into MHC II molecules, increased acidification produces increased proteolysis and efficient peptide loading.
+== 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/t5/1t5x_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=1t5x ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Peptides bind to class II major histocompatibility complex (MHC) proteins in an extended conformation. Pockets in the peptide binding site spaced to accommodate peptide side chains at the P1, P4, P6, and P9 positions have been previously characterized and help to explain the obtained peptide binding specificity. However, two peptides differing only at P10 have significantly different binding affinities for HLA-DR1. The structure of HLA-DR1 in complex with the tighter binding peptide shows that the peptide binds in the usual polyproline type II conformation, but with the P10 residue accommodated in a shallow pocket at the end of the binding groove. HLA-DR1 variants with polymorphic residues at these positions were produced and found to exhibit different side chain specificity at the P10 position. These results define a new specificity position in HLA-DR proteins.
-===HLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR) and the superantigen SEC3-3B2===
+A polymorphic pocket at the P10 position contributes to peptide binding specificity in class II MHC proteins.,Zavala-Ruiz Z, Strug I, Anderson MW, Gorski J, Stern LJ Chem Biol. 2004 Oct;11(10):1395-402. PMID:15489166<ref>PMID:15489166</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1t5x" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15489166}}, adds the Publication Abstract to the page
+*[[MHC 3D structures|MHC 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15489166 is the PubMed ID number.
+*[[MHC II 3D structures|MHC II 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_15489166}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-T5X is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T5X OCA].
-==Reference==
-<ref group="xtra">PMID:15489166</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Saccharomyces cerevisiae S288C]]
 [[Category: Staphylococcus aureus]]
-[[Category: Anderson, M W.]]
+[[Category: Anderson MW]]
-[[Category: Gorski, J.]]
+[[Category: Gorski J]]
-[[Category: Stern, L J.]]
+[[Category: Stern LJ]]
-[[Category: Strug, I.]]
+[[Category: Strug I]]
-[[Category: Zavala-Ruiz, Z.]]
+[[Category: Zavala-Ruiz Z]]
-[[Category: Antigen]]
-[[Category: Hla-dr1]]
-[[Category: Major histocompatibiloty complex protein]]
-[[Category: Mhc class ii]]
-[[Category: Peptide]]
-[[Category: Superantigen]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 19:47:58 2009''