2ja8

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==CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX D==
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<StructureSection load='2ja8' size='340' side='right' caption='[[2ja8]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
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==CPD lesion containing RNA Polymerase II elongation complex D==
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<StructureSection load='2ja8' size='340' side='right'caption='[[2ja8]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[2ja8]] is a 15 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=2JA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JA8 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[2ja8]] 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=2JA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JA8 FirstGlance]. <br>
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</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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.8&#8491;</td></tr>
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<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>
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<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>
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<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]], [[2ja7|2ja7]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ja8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ja8 OCA], [https://pdbe.org/2ja8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ja8 RCSB], [https://www.ebi.ac.uk/pdbsum/2ja8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ja8 ProSAT]</span></td></tr>
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<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>
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</table>
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<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=2ja8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ja8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ja8 RCSB], [http://www.ebi.ac.uk/pdbsum/2ja8 PDBsum]</span></td></tr>
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== Function ==
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<table>
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[https://www.uniprot.org/uniprot/RPB2_YEAST RPB2_YEAST] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw. The jaws are thought to grab the incoming DNA template. The fork loop 1 (RPB2) interacts with the RNA-DNA hybrid, possibly stabilizing it.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
<jmolCheckbox>
<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ja/2ja8_consurf.spt"</scriptWhenChecked>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ja/2ja8_consurf.spt"</scriptWhenChecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
<text>to colour the structure by Evolutionary Conservation</text>
<text>to colour the structure by Evolutionary Conservation</text>
</jmolCheckbox>
</jmolCheckbox>
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</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].
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</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=2ja8 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
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<div class="pdbe-citations 2ja8" style="background-color:#fffaf0;"></div>
==See Also==
==See Also==
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*[[RNA polymerase|RNA polymerase]]
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Brueckner, F.]]
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[[Category: Synthetic construct]]
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[[Category: Carell, T.]]
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[[Category: Brueckner F]]
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[[Category: Cramer, P.]]
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[[Category: Carell T]]
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[[Category: Hennecke, U.]]
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[[Category: Cramer P]]
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[[Category: Arrest]]
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[[Category: Hennecke U]]
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[[Category: Cpd]]
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[[Category: Cyclobutane pyrimidine dimer tcr]]
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[[Category: Damage recognition]]
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[[Category: Dna damage]]
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[[Category: Dna lesion]]
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[[Category: Dna-binding]]
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[[Category: Dna-directed rna polymerase]]
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[[Category: Elongation complex]]
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[[Category: Lesion recognition]]
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[[Category: Metal-binding]]
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[[Category: Misincorporation]]
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[[Category: Nuclear protein]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Phosphorylation]]
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[[Category: Photolesion]]
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[[Category: Rna polymerase ii]]
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[[Category: Stalling]]
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[[Category: Thymine dimer]]
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[[Category: Transcription]]
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[[Category: Transcription bubble]]
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[[Category: Transcription-coupled repair]]
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[[Category: Transferase]]
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[[Category: Transferase/dna/rna]]
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[[Category: Zinc-finger]]
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Current revision

CPD lesion containing RNA Polymerase II elongation complex D

PDB ID 2ja8

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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