2ja7: Difference between revisions

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-[[Image:2ja7.png|left|200px]]
+==CPD lesion containing RNA Polymerase II elongation complex C==
+<StructureSection load='2ja7' size='340' side='right' caption='[[2ja7]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2ja7]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JA7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JA7 FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
+<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=TT:'>TT</scene></td></tr>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1i3q|1i3q]], [[1i50|1i50]], [[1i6h|1i6h]], [[1k83|1k83]], [[1nik|1nik]], [[1nt9|1nt9]], [[1pqv|1pqv]], [[1r5u|1r5u]], [[1r9s|1r9s]], [[1r9t|1r9t]], [[1sfo|1sfo]], [[1twa|1twa]], [[1twc|1twc]], [[1twf|1twf]], [[1twg|1twg]], [[1twh|1twh]], [[1wcm|1wcm]], [[1y1v|1y1v]], [[1y1w|1y1w]], [[1y1y|1y1y]], [[1y77|1y77]], [[2b63|2b63]], [[2b8k|2b8k]], [[1dzf|1dzf]], [[1a1d|1a1d]], [[1y14|1y14]], [[2ja5|2ja5]], [[2ja6|2ja6]], [[2ja8|2ja8]]</td></tr>
+<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ja7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ja7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ja7 RCSB], [http://www.ebi.ac.uk/pdbsum/2ja7 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/ja/2ja7_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 ==
+Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA lesions such as ultraviolet light-induced cyclobutane pyrimidine dimers (CPDs). Here we present the structure-based mechanism for the first step in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II. A CPD in the transcribed strand slowly passes a translocation barrier and enters the polymerase active site. The CPD 5'-thymine then directs uridine misincorporation into messenger RNA, which blocks translocation. Artificial replacement of the uridine by adenosine enables CPD bypass; thus, Pol II stalling requires CPD-directed misincorporation. In the stalled complex, the lesion is inaccessible, and the polymerase conformation is unchanged. This is consistent with nonallosteric recruitment of repair factors and excision of a lesion-containing DNA fragment in the presence of Pol II.
-{{STRUCTURE_2ja7|  PDB=2ja7  |  SCENE=  }}
+CPD damage recognition by transcribing RNA polymerase II.,Brueckner F, Hennecke U, Carell T, Cramer P Science. 2007 Feb 9;315(5813):859-62. PMID:17290000<ref>PMID:17290000</ref>
-===CPD lesion containing RNA Polymerase II elongation complex C===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_17290000}}
-==About this Structure==
-[[2ja7]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JA7 OCA].
 ==See Also==
 *[[RNA polymerase|RNA polymerase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017290000</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: DNA-directed RNA polymerase]]
 [[Category: Saccharomyces cerevisiae]]