2ja6: Difference between revisions

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-{{Seed}}
-[[Image:2ja6.png|left|200px]]
-<!--
+==CPD lesion containing RNA Polymerase II elongation complex B==
-The line below this paragraph, containing "STRUCTURE_2ja6", creates the "Structure Box" on the page.
+<StructureSection load='2ja6' size='340' side='right'caption='[[2ja6]], [[Resolution|resolution]] 4.00&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'>[[2ja6]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JA6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JA6 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]] 4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TT:[(1R,3R,4S,9R,10S,12R,15aS,15bR,18bR,18cS)-10-hydroxy-15a,15b-dimethyl-13,15,16,18-tetraoxohexadecahydro-8H-9,12-epoxy-1,4-methano-2,5,7-trioxa-12a,14,17,18a-tetraazacyclohexadeca[1,2,3,4-def]biphenylen-3-yl]methyl+dihydrogen+phosphate'>TT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2ja6|  PDB=2ja6  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ja6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ja6 OCA], [https://pdbe.org/2ja6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ja6 RCSB], [https://www.ebi.ac.uk/pdbsum/2ja6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ja6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RPB3_YEAST RPB3_YEAST] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft. Seems to be involved in transcription termination.
+== 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/2ja6_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=2ja6 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.
-===CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX B===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ja6" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17290000}}, adds the Publication Abstract to the page
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17290000 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17290000}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-JA6 is a 15 chains structure of sequences 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=2JA6 OCA].
-==Reference==
-<ref group="xtra">PMID:17290000</ref><references group="xtra"/>
-[[Category: DNA-directed RNA polymerase]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Brueckner, F.]]
+[[Category: Synthetic construct]]
-[[Category: Carell, T.]]
+[[Category: Brueckner F]]
-[[Category: Cramer, P.]]
+[[Category: Carell T]]
-[[Category: Hennecke, U.]]
+[[Category: Cramer P]]
-[[Category: Arrest]]
+[[Category: Hennecke U]]
-[[Category: Cpd]]
-[[Category: Cyclobutane pyrimidine dimer]]
-[[Category: Damage recognition]]
-[[Category: Dna damage]]
-[[Category: Dna lesion]]
-[[Category: Dna-binding]]
-[[Category: Dna-directed rna polymerase]]
-[[Category: Elongation complex]]
-[[Category: Lesion recognition]]
-[[Category: Metal-binding]]
-[[Category: Misincorporation]]
-[[Category: Nuclear protein]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Phosphorylation]]
-[[Category: Photolesion]]
-[[Category: Rna polymerase ii]]
-[[Category: Stalling]]
-[[Category: Tcr]]
-[[Category: Thymine dimer]]
-[[Category: Transcription]]
-[[Category: Transcription bubble]]
-[[Category: Transcription- coupled repair]]
-[[Category: Transferase]]
-[[Category: Transferase/dna/rna]]
-[[Category: Zinc]]
-[[Category: Zinc-finger]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 01:48:19 2009''