1l9z - Revision history

OCA at 07:31, 14 February 2024

OCA — Wed, 14 Feb 2024 07:31:17 GMT

←Older revision		Revision as of 07:31, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1l9z' size='340' side='right'caption='[[1l9z]], [[Resolution\|resolution]] 6.50Å' scene=''>		<StructureSection load='1l9z' size='340' side='right'caption='[[1l9z]], [[Resolution\|resolution]] 6.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l9z]] is a 8 chain structure with sequence from [~~http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104] and [http~~://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1L9Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l9z]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L9Z 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">X-ray diffraction, [[Resolution\|Resolution]] 6.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~271 ATCC 25104])</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~~'>~~[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'>[https://proteopedia.org/fgij/fg.htm?mol=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [https://pdbe.org/1l9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [https://www.ebi.ac.uk/pdbsum/1l9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l9z 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=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [~~http~~://pdbe.org/1l9z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1l9z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1l9z ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RPOZ_THEAQ RPOZ_THEAQ]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.<ref>PMID:11158566</ref> [[http://www.uniprot.org/uniprot/Q9EZJ8_THEAQ Q9EZJ8_THEAQ]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity).[RuleBase:RU000715]	+	[https://www.uniprot.org/uniprot/RPOA_THEAQ RPOA_THEAQ]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=1l9z ConSurf].		</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=1l9z ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of Thermus aquaticus RNA polymerase holoenzyme (alpha2betabeta'omegasigmaA) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures of individual components into a 6.5-angstrom resolution map. The DNA lies across one face of the holoenzyme, completely outside the RNA polymerase active site channel. All sequence-specific contacts with core promoter elements are mediated by the sigma subunit. A universally conserved tryptophan is ideally positioned to stack on the exposed face of the base pair at the upstream edge of the transcription bubble. Universally conserved basic residues of the sigma subunit provide critical contacts with the DNA phosphate backbone and play a role in directing the melted DNA template strand into the RNA polymerase active site. The structure explains how holoenzyme recognizes promoters containing variably spaced -10 and -35 elements and provides the basis for models of the closed and open promoter complexes.
-
-	Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex.,Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA Science. 2002 May 17;296(5571):1285-90. PMID:12016307<ref>PMID:12016307</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1l9z" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]		*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	*[[Sigma factor 3D structures\|Sigma factor 3D structures]]		*[[Sigma factor 3D structures\|Sigma factor 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 25104]]
-	[[Category: DNA-directed RNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
-	[[Category: Campbell~~, E A~~]]	+	[[Category: Campbell EA]]
-	[[Category: Darst~~, S A~~]]	+	[[Category: Darst SA]]
-	[[Category: Masuda, S]]	+	[[Category: Masuda S]]
-	[[Category: Murakami~~, K S~~]]	+	[[Category: Murakami KS]]
-	[[Category: Muzzin, O]]	+	[[Category: Muzzin O]]
-	~~[[Category: Coiled-coil]]~~	+
-	~~[[Category: Helix-turn-helix]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 07:57, 25 November 2020

OCA — Wed, 25 Nov 2020 07:57:03 GMT

←Older revision		Revision as of 07:57, 25 November 2020
Line 1:		Line 1:

	==Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution==		==Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution==
-	<StructureSection load='1l9z' size='340' side='right' caption='[[1l9z]], [[Resolution\|resolution]] 6.50Å' scene=''>	+	<StructureSection load='1l9z' size='340' side='right'caption='[[1l9z]], [[Resolution\|resolution]] 6.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l9z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1L9Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l9z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1L9Z 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</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=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [http://pdbe.org/1l9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [http://www.ebi.ac.uk/pdbsum/1l9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l9z 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=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [http://pdbe.org/1l9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [http://www.ebi.ac.uk/pdbsum/1l9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l9z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1l9z" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1l9z" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
		+	*[[Sigma factor 3D structures\|Sigma factor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 40:
	[[Category: Atcc 25104]]		[[Category: Atcc 25104]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
	[[Category: Campbell, E A]]		[[Category: Campbell, E A]]

OCA at 21:37, 24 January 2018

OCA — Wed, 24 Jan 2018 21:37:40 GMT

←Older revision		Revision as of 21:37, 24 January 2018
Line 1:		Line 1:
		+
	==Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution==		==Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution==
	<StructureSection load='1l9z' size='340' side='right' caption='[[1l9z]], [[Resolution\|resolution]] 6.50Å' scene=''>		<StructureSection load='1l9z' size='340' side='right' caption='[[1l9z]], [[Resolution\|resolution]] 6.50Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</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=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [http://pdbe.org/1l9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [http://www.ebi.ac.uk/pdbsum/1l9z 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=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [http://pdbe.org/1l9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [http://www.ebi.ac.uk/pdbsum/1l9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l9z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l9/1l9z_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l9/1l9z_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>
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1l9z" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1l9z" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[RNA polymerase\|RNA polymerase]]
-	*[[Sigma factor\|Sigma factor]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 22:11, 8 February 2016

OCA — Mon, 08 Feb 2016 22:11:09 GMT

←Older revision		Revision as of 22:11, 8 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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].	+	</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=1l9z ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:50, 10 September 2015

OCA — Thu, 10 Sep 2015 15:50:25 GMT

←Older revision		Revision as of 15:50, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1l9z' size='340' side='right' caption='[[1l9z]], [[Resolution\|resolution]] 6.50Å' scene=''>		<StructureSection load='1l9z' size='340' side='right' caption='[[1l9z]], [[Resolution\|resolution]] 6.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l9z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L9Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l9z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104] and [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L9Z 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"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ~~Thermus aquaticus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</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=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [http://www.ebi.ac.uk/pdbsum/1l9z 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=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [http://pdbe.org/1l9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [http://www.ebi.ac.uk/pdbsum/1l9z PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1l9z" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
		+	*[[Sigma factor\|Sigma factor]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 25104]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]

OCA at 02:28, 25 December 2014

OCA — Thu, 25 Dec 2014 02:28:17 GMT

←Older revision		Revision as of 02:28, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1l9z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L9Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[1l9z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L9Z 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>	+	</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><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</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 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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [http://www.ebi.ac.uk/pdbsum/1l9z 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=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [http://www.ebi.ac.uk/pdbsum/1l9z PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPOZ_THEAQ RPOZ_THEAQ]] Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits.<ref>PMID:11158566</ref> [[http://www.uniprot.org/uniprot/Q9EZJ8_THEAQ Q9EZJ8_THEAQ]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity).[RuleBase:RU000715]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
-	[[Category: Campbell, E A.]]	+	[[Category: Campbell, E A]]
-	[[Category: Darst, S A.]]	+	[[Category: Darst, S A]]
-	[[Category: Masuda, S.]]	+	[[Category: Masuda, S]]
-	[[Category: Murakami, K S.]]	+	[[Category: Murakami, K S]]
-	[[Category: Muzzin, O.]]	+	[[Category: Muzzin, O]]
	[[Category: Coiled-coil]]		[[Category: Coiled-coil]]
	[[Category: Helix-turn-helix]]		[[Category: Helix-turn-helix]]
	[[Category: Transcription-dna complex]]		[[Category: Transcription-dna complex]]

OCA at 18:20, 28 September 2014

OCA — Sun, 28 Sep 2014 18:20:23 GMT

←Older revision		Revision as of 18:20, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1l9z.~~png~~\|~~left~~\|200px]]	+	==Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution==
		+	<StructureSection load='1l9z' size='340' side='right' caption='[[1l9z]], [[Resolution\|resolution]] 6.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1l9z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L9Z 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>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</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=1l9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l9z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l9z RCSB], [http://www.ebi.ac.uk/pdbsum/1l9z 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/l9/1l9z_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 crystal structure of Thermus aquaticus RNA polymerase holoenzyme (alpha2betabeta'omegasigmaA) complexed with a fork-junction promoter DNA fragment has been determined by fitting high-resolution x-ray structures of individual components into a 6.5-angstrom resolution map. The DNA lies across one face of the holoenzyme, completely outside the RNA polymerase active site channel. All sequence-specific contacts with core promoter elements are mediated by the sigma subunit. A universally conserved tryptophan is ideally positioned to stack on the exposed face of the base pair at the upstream edge of the transcription bubble. Universally conserved basic residues of the sigma subunit provide critical contacts with the DNA phosphate backbone and play a role in directing the melted DNA template strand into the RNA polymerase active site. The structure explains how holoenzyme recognizes promoters containing variably spaced -10 and -35 elements and provides the basis for models of the closed and open promoter complexes.

-	~~{{STRUCTURE_1l9z\| PDB=1l9z \| SCENE= }}~~	+	Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex.,Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA Science. 2002 May 17;296(5571):1285-90. PMID:12016307<ref>PMID:12016307</ref>

-	~~===Thermus aquaticus RNA Polymerase Holoenzyme~~/~~Fork-Junction Promoter DNA Complex at 6.5 A Resolution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12016307}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1l9z]] is~~ a ~~8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_aquaticus Thermus aquaticus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA].~~	+

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012016307<~~/~~ref~~><~~ref group="xtra">PMID:014704342</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]

OCA at 11:38, 20 October 2012

OCA — Sat, 20 Oct 2012 11:38:35 GMT

←Older revision		Revision as of 11:38, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1l9z]] is a 8 chain structure ~~of [[RNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA].	+	[[1l9z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA].

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

OCA: Protected "1l9z" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 06:04:53 GMT

Protected "1l9z" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:04, 26 July 2012

OCA at 06:04, 26 July 2012

OCA — Thu, 26 Jul 2012 06:04:51 GMT

←Older revision		Revision as of 06:04, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1l9z.png\|left\|200px]]		[[Image:1l9z.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1l9z", creates the "Structure Box" on the page.
-	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),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1l9z\| PDB=1l9z \| SCENE= }}		{{STRUCTURE_1l9z\| PDB=1l9z \| SCENE= }}

	===Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution===		===Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A Resolution===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12016307}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12016307 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12016307}}		{{ABSTRACT_PUBMED_12016307}}

	==About this Structure==		==About this Structure==
-	~~1L9Z~~ is a 8 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA].	+	[[1l9z]] is a 8 chain structure of [[RNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L9Z OCA].
		+
		+	==See Also==
		+	*[[RNA polymerase\|RNA polymerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12016307~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012016307</ref><ref group="xtra">PMID:014704342</ref><references group="xtra"/>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
Line 33:		Line 24:
	[[Category: Coiled-coil]]		[[Category: Coiled-coil]]
	[[Category: Helix-turn-helix]]		[[Category: Helix-turn-helix]]
-		+	[[Category: Transcription-dna complex]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 03:54:09 2009''~~	+