1lnu: Difference between revisions

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-[[Image:1lnu.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1lnu", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1lnu|  PDB=1lnu  |  SCENE=  }}
-'''CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IAb BOUND TO EALPHA3K PEPTIDE'''
+==CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IAb BOUND TO EALPHA3K PEPTIDE==
+<StructureSection load='1lnu' size='340' side='right'caption='[[1lnu]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1lnu]] is a 8 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=1LNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LNU FirstGlance]. <br>
+</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=1lnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lnu OCA], [https://pdbe.org/1lnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lnu RCSB], [https://www.ebi.ac.uk/pdbsum/1lnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lnu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HA2B_MOUSE HA2B_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/ln/1lnu_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=1lnu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have solved the crystal structure of the MHCII molecule, IA(b), containing an antigenic variant of the major IA(b)-binding peptide derived from the MHCII IEalpha chain. The four MHC pockets at p1, p4, p6, and p9 that usually bind peptide side chains are largely empty because of alanines in the peptide at these positions. The complex is nevertheless very stable, apparently because of unique alternate interactions between the IA(b) and peptide. In particular, there are multiple additional hydrogen bonds between the N-terminal end of the peptide and the IA(b) alpha chain and an extensive hydrogen bond network involving an asparagine at p7 position of the peptide and the IA(b) beta chain. By using knowledge of the shape and size of the traditional side chain binding pockets and the additional possible interactions, an IA(b) peptide-binding motif can be deduced that agrees well with the sequences of known IA(b)-binding peptides.
-==Overview==
+Alternate interactions define the binding of peptides to the MHC molecule IA(b).,Liu X, Dai S, Crawford F, Fruge R, Marrack P, Kappler J Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8820-5. PMID:12084926<ref>PMID:12084926</ref>
-We have solved the crystal structure of the MHCII molecule, IA(b), containing an antigenic variant of the major IA(b)-binding peptide derived from the MHCII IEalpha chain. The four MHC pockets at p1, p4, p6, and p9 that usually bind peptide side chains are largely empty because of alanines in the peptide at these positions. The complex is nevertheless very stable, apparently because of unique alternate interactions between the IA(b) and peptide. In particular, there are multiple additional hydrogen bonds between the N-terminal end of the peptide and the IA(b) alpha chain and an extensive hydrogen bond network involving an asparagine at p7 position of the peptide and the IA(b) beta chain. By using knowledge of the shape and size of the traditional side chain binding pockets and the additional possible interactions, an IA(b) peptide-binding motif can be deduced that agrees well with the sequences of known IA(b)-binding peptides.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-LNU is a [[Protein complex]] 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=1LNU OCA].
+</div>
+<div class="pdbe-citations 1lnu" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Alternate interactions define the binding of peptides to the MHC molecule IA(b)., Liu X, Dai S, Crawford F, Fruge R, Marrack P, Kappler J, Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8820-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12084926 12084926]
+*[[MHC 3D structures|MHC 3D structures]]
+*[[MHC II 3D structures|MHC II 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Protein complex]]
+[[Category: Crawford F]]
-[[Category: Crawford, F.]]
+[[Category: Dai S]]
-[[Category: Dai, S.]]
+[[Category: Fruge R]]
-[[Category: Fruge, R.]]
+[[Category: Kappler J]]
-[[Category: Kappler, J.]]
+[[Category: Liu X]]
-[[Category: Liu, X.]]
+[[Category: Marrack P]]
-[[Category: Marrack, P.]]
-[[Category: Antigen presentation]]
-[[Category: Protein-peptide complex]]
-[[Category: T cell receptor]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 00:05:53 2008''