3lyr: Difference between revisions

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-{{STRUCTURE_3lyr|  PDB=3lyr  |  SCENE=  }}
+==Human Early B-cell Factor 1 (EBF1) DNA-binding domain==
-===Human Early B-cell Factor 1 (EBF1) DNA-binding domain===
+<StructureSection load='3lyr' size='340' side='right' caption='[[3lyr]], [[Resolution|resolution]] 2.51&Aring;' scene=''>
-{{ABSTRACT_PUBMED_20592035}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3lyr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LYR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LYR FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">COE1, EBF, EBF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3lyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lyr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lyr RCSB], [http://www.ebi.ac.uk/pdbsum/3lyr PDBsum]</span></td></tr>
+</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/ly/3lyr_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/chain_selection.php?pdb_ID=2ata ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The early B-cell factor (EBF) transcription factors are central regulators of development in several organs and tissues. This protein family shows low sequence similarity to other protein families, which is why structural information for the functional domains of these proteins is crucial to understand their biochemical features. We have used a modular approach to determine the crystal structures of the structured domains in the EBF family. The DNA binding domain reveals a striking resemblance to the DNA binding domains of the Rel homology superfamily of transcription factors but contains a unique zinc binding structure, termed zinc knuckle. Further the EBF proteins contain an IPT/TIG domain and an atypical helix-loop-helix domain with a novel type of dimerization motif. The data presented here provide insights into unique structural features of the EBF proteins and open possibilities for detailed molecular investigations of this important transcription factor family.
-==Function==
+Structural determination of functional domains in early B-cell factor (EBF) family of transcription factors reveals similarities to Rel DNA-binding proteins and a novel dimerization motif.,Siponen MI, Wisniewska M, Lehtio L, Johansson I, Svensson L, Raszewski G, Nilsson L, Sigvardsson M, Berglund H J Biol Chem. 2010 Aug 20;285(34):25875-9. Epub 2010 Jun 30. PMID:20592035<ref>PMID:20592035</ref>
-[[http://www.uniprot.org/uniprot/COE1_HUMAN COE1_HUMAN]] Transcriptional activator which recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity).
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[3lyr]] is a 1 chain structure with 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=3LYR OCA].
+</div>
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020592035</ref><references group="xtra"/><references/>
+__TOC__
-[[Category: Homo sapiens]]
+</StructureSection>
+[[Category: Human]]
 [[Category: Arrowsmith, C H.]]
 [[Category: Berg, S Van Den.]]
@@ Line 32: / Line 51: @@
 [[Category: Persson, C.]]
 [[Category: SGC, Structural Genomics Consortium.]]
-[[Category: Schuler, H]]
+[[Category: Schuler, H.]]
 [[Category: Schutz, P.]]
 [[Category: Siponen, M I.]]
 [[Category: Svensson, L.]]
-[[Category: Thorsell, A G]]
+[[Category: Thorsell, A G.]]
 [[Category: Tresaugues, L.]]
-[[Category: Wahlberg, E]]
+[[Category: Wahlberg, E.]]
 [[Category: Weigelt, J.]]
 [[Category: Welin, M.]]