3j0k - Revision history

OCA at 14:12, 24 January 2024

2024-01-24T14:12:39Z

←Older revision		Revision as of 14:12, 24 January 2024
Line 3:		Line 3:
	<SX load='3j0k' size='340' side='right' viewer='molstar' caption='[[3j0k]], [[Resolution\|resolution]] 36.00Å' scene=''>		<SX load='3j0k' size='340' side='right' viewer='molstar' caption='[[3j0k]], [[Resolution\|resolution]] 36.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j0k]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J0K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j0k]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J0K FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 36Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1y1v\|1y1v]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j0k OCA], [https://pdbe.org/3j0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j0k RCSB], [https://www.ebi.ac.uk/pdbsum/3j0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j0k ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j0k OCA], [https://pdbe.org/3j0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j0k RCSB], [https://www.ebi.ac.uk/pdbsum/3j0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j0k ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 26:
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: DNA-directed RNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bernecky, C]]	+	[[Category: Bernecky C]]
-	[[Category: Ebmeier~~, C C~~]]	+	[[Category: Ebmeier CC]]
-	[[Category: Grob, P]]	+	[[Category: Grob P]]
-	[[Category: Nogales, E]]	+	[[Category: Nogales E]]
-	[[Category: Taatjes~~, D J]]~~	+	[[Category: Taatjes DJ]]
-	~~[[Category: Transferase-transcription complex~~]]	+

OCA at 03:47, 21 April 2022

2022-04-21T03:47:20Z

←Older revision		Revision as of 03:47, 21 April 2022
Line 3:		Line 3:
	<SX load='3j0k' size='340' side='right' viewer='molstar' caption='[[3j0k]], [[Resolution\|resolution]] 36.00Å' scene=''>		<SX load='3j0k' size='340' side='right' viewer='molstar' caption='[[3j0k]], [[Resolution\|resolution]] 36.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j0k]] is a 12 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=3J0K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3J0K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j0k]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J0K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3J0K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1y1v\|1y1v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1y1v\|1y1v]]</div></td></tr>
-	<tr id='activity'><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 id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j0k OCA], [~~http~~://pdbe.org/3j0k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3j0k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3j0k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3j0k ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j0k OCA], [https://pdbe.org/3j0k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3j0k RCSB], [https://www.ebi.ac.uk/pdbsum/3j0k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3j0k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:39, 10 April 2020

2020-04-10T17:39:13Z

←Older revision		Revision as of 17:39, 10 April 2020
Line 3:		Line 3:
	<SX load='3j0k' size='340' side='right' viewer='molstar' caption='[[3j0k]], [[Resolution\|resolution]] 36.00Å' scene=''>		<SX load='3j0k' size='340' side='right' viewer='molstar' caption='[[3j0k]], [[Resolution\|resolution]] 36.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3j0k]] is a 12 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=3J0K OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3J0K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3j0k]] is a 12 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=3J0K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3J0K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><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></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1y1v\|1y1v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1y1v\|1y1v]]</td></tr>
	<tr id='activity'><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 id='activity'><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 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=3j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j0k OCA], [http://pdbe.org/3j0k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j0k RCSB], [http://www.ebi.ac.uk/pdbsum/3j0k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j0k ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j0k OCA], [http://pdbe.org/3j0k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j0k RCSB], [http://www.ebi.ac.uk/pdbsum/3j0k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j0k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:15, 6 March 2020

2020-03-06T17:15:38Z

←Older revision		Revision as of 17:15, 6 March 2020
Line 1:		Line 1:

	==Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly==		==Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly==
-	<~~StructureSection~~ load='3j0k' size='340' side='right' caption='[[3j0k]], [[Resolution\|resolution]] 36.00Å' scene=''>	+	<SX load='3j0k' size='340' side='right' viewer='molstar' caption='[[3j0k]], [[Resolution\|resolution]] 36.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3j0k]] is a 12 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=3J0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J0K FirstGlance]. <br>		<table><tr><td colspan='2'>[[3j0k]] is a 12 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=3J0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J0K FirstGlance]. <br>
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[RNA polymerase\|RNA polymerase]]	+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
	[[Category: Bernecky, C]]		[[Category: Bernecky, C]]
	[[Category: Ebmeier, C C]]		[[Category: Ebmeier, C C]]

OCA at 20:27, 9 December 2016

2016-12-09T20:27:07Z

←Older revision		Revision as of 20:27, 9 December 2016
Line 1:		Line 1:
		+
	==Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly==		==Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly==
	<StructureSection load='3j0k' size='340' side='right' caption='[[3j0k]], [[Resolution\|resolution]] 36.00Å' scene=''>		<StructureSection load='3j0k' size='340' side='right' caption='[[3j0k]], [[Resolution\|resolution]] 36.00Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1y1v\|1y1v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1y1v\|1y1v]]</td></tr>
	<tr id='activity'><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 id='activity'><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 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=3j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j0k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j0k RCSB], [http://www.ebi.ac.uk/pdbsum/3j0k PDBsum]</span></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=3j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j0k OCA], [http://pdbe.org/3j0k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j0k RCSB], [http://www.ebi.ac.uk/pdbsum/3j0k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j0k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3j0k" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 09:27, 8 December 2014

2014-12-08T09:27:17Z

←Older revision		Revision as of 09:27, 8 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3j0k.~~png~~\|~~left~~\|~~200px~~]]	+	==Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly==
		+	<StructureSection load='3j0k' size='340' side='right' caption='[[3j0k]], [[Resolution\|resolution]] 36.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3j0k]] is a 12 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=3J0K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J0K FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><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></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1y1v\|1y1v]]</td></tr>
		+	<tr id='activity'><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 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=3j0k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j0k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3j0k RCSB], [http://www.ebi.ac.uk/pdbsum/3j0k PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly.

-	~~{{STRUCTURE_3j0k\| PDB=3j0k \| SCENE= }}~~	+	Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.,Bernecky C, Grob P, Ebmeier CC, Nogales E, Taatjes DJ PLoS Biol. 2011 Mar;9(3):e1000603. Epub 2011 Mar 29. PMID:21468301<ref>PMID:21468301</ref>

-	~~===Orientation~~ of ~~RNA polymerase II within~~ the ~~human VP16-Mediator-pol II-TFIIF assembly===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21468301}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3j0k]] is a 12 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=3J0K OCA].~~	+

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:021468301<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Bernecky, C.]]	+	[[Category: Bernecky, C]]
-	[[Category: Ebmeier, C C.]]	+	[[Category: Ebmeier, C C]]
-	[[Category: Grob, P.]]	+	[[Category: Grob, P]]
-	[[Category: Nogales, E.]]	+	[[Category: Nogales, E]]
-	[[Category: Taatjes, D J.]]	+	[[Category: Taatjes, D J]]
	[[Category: Transferase-transcription complex]]		[[Category: Transferase-transcription complex]]

OCA at 17:00, 20 October 2012

2012-10-20T17:00:09Z

←Older revision		Revision as of 17:00, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3j0k]] is a 12 chain structure ~~of [[RNA polymerase]]~~ 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=3J0K OCA].	+	[[3j0k]] is a 12 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=3J0K OCA].

	==See Also==		==See Also==

OCA at 23:30, 26 July 2012

2012-07-26T23:30:49Z

←Older revision		Revision as of 23:30, 26 July 2012
Line 1:		Line 1:
	[[Image:3j0k.png\|left\|200px]]		[[Image:3j0k.png\|left\|200px]]

-	<!--
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-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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	{{STRUCTURE_3j0k\| PDB=3j0k \| SCENE= }}		{{STRUCTURE_3j0k\| PDB=3j0k \| SCENE= }}

	===Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly===		===Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21468301}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21468301 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_21468301}}		{{ABSTRACT_PUBMED_21468301}}

	==About this Structure==		==About this Structure==
-	[[3j0k]] is a 12 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=3J0K OCA].	+	[[3j0k]] is a 12 chain structure of [[RNA polymerase]] 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=3J0K OCA].
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]

	==Reference==		==Reference==

OCA: Protected "3j0k" [edit=sysop:move=sysop]

2011-10-30T07:45:27Z

Protected "3j0k" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:45, 30 October 2011