3e6j: Difference between revisions

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-[[Image:3e6j.png|left|200px]]
-<!--
+==Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 in Complex with H-trisaccharide==
-The line below this paragraph, containing "STRUCTURE_3e6j", creates the "Structure Box" on the page.
+<StructureSection load='3e6j' size='340' side='right'caption='[[3e6j]], [[Resolution|resolution]] 1.67&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'>[[3e6j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3E6J 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]] 1.67&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3e6j|  PDB=3e6j  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3e6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e6j OCA], [https://pdbe.org/3e6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e6j RCSB], [https://www.ebi.ac.uk/pdbsum/3e6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e6j ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q2VGE8_PETMA Q2VGE8_PETMA]
+== 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/e6/3e6j_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=3e6j ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Variable lymphocyte receptors (VLRs) rather than antibodies play the primary role in recognition of antigens in the adaptive immune system of jawless vertebrates. Combinatorial assembly of leucine-rich repeat (LRR) gene segments achieves the required repertoire for antigen recognition. We have determined a crystal structure for a VLR-antigen complex, VLR RBC36 in complex with the H-antigen trisaccharide from human blood type O erythrocytes, at 1.67 angstrom resolution. RBC36 binds the H-trisaccharide on the concave surface of the LRR modules of the solenoid structure where three key hydrophilic residues, multiple van der Waals interactions, and the highly variable insert of the carboxyl-terminal LRR module determine antigen recognition and specificity. The concave surface assembled from the most highly variable regions of the LRRs, along with diversity in the sequence and length of the highly variable insert, can account for the recognition of diverse antigens by VLRs.
-===Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 in Complex with H-trisaccharide===
+Antigen recognition by variable lymphocyte receptors.,Han BW, Herrin BR, Cooper MD, Wilson IA Science. 2008 Sep 26;321(5897):1834-7. PMID:18818359<ref>PMID:18818359</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18818359}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3e6j" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18818359 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_18818359}}
-==About this Structure==
-[[3e6j]] is a 1 chain structure of [[Lamprey Variable Lymphocyte Receptor]] and [[Variable lymphocyte receptor]] with sequence from [http://en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E6J OCA].
 ==See Also==
 *[[Lamprey Variable Lymphocyte Receptor|Lamprey Variable Lymphocyte Receptor]]
-*[[Variable lymphocyte receptor|Variable lymphocyte receptor]]
+*[[Variable lymphocyte receptor 3D structures|Variable lymphocyte receptor 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018818359</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Petromyzon marinus]]
-[[Category: Cooper, M D.]]
+[[Category: Cooper MD]]
-[[Category: Han, B W.]]
+[[Category: Han BW]]
-[[Category: Herrin, B R.]]
+[[Category: Herrin BR]]
-[[Category: Wilson, I A.]]
+[[Category: Wilson IA]]
-[[Category: Adaptive immunity]]
-[[Category: Immune system]]
-[[Category: Jawless fish]]
-[[Category: Leucine-rich repeat]]
-[[Category: Lrr]]
-[[Category: Receptor]]
-[[Category: Sea lamprey]]
-[[Category: Variable lymphocyte receptor]]
-[[Category: Vlr]]