4xls - Revision history

OCA at 17:42, 26 April 2023

2023-04-26T17:42:18Z

←Older revision		Revision as of 17:42, 26 April 2023
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	==Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter.==		==Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter.==
-	<StructureSection load='4xls' size='340' side='right' caption='[[4xls]], [[Resolution\|resolution]] 4.01Å' scene=''>	+	<StructureSection load='4xls' size='340' side='right'caption='[[4xls]], [[Resolution\|resolution]] 4.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xls]] is a 18 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_25104 Atcc 25104~~], [~~http~~://en.wikipedia.org/wiki/~~Thermus_aquaticus~~ Thermus ~~aquaticus~~] and [~~http~~://en.wikipedia.org/wiki/~~Thermus_thermophilus_jl-18 Thermus thermophilus jl-18~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XLS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XLS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xls]] is a 18 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus], [https://en.wikipedia.org/wiki/Thermus_thermophilus_JL-18 Thermus thermophilus JL-18] 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=4XLS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XLS 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">[[4xln\|4xln]], [[4xlp\|4xlp]], [[4xlq\|4xlq]], [[4xlr\|4xlr]], [[4xax\|4xax]]</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=4xls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xls OCA], [https://pdbe.org/4xls PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xls RCSB], [https://www.ebi.ac.uk/pdbsum/4xls PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xls ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sigA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104]), TtJL18_0238 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=798128 Thermus thermophilus JL-18])</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=4xls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xls OCA], [~~http~~://pdbe.org/4xls PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xls RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xls PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xls 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/SIGA_THEAQ SIGA_THEAQ]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.[HAMAP-Rule:MF_00963]<ref>PMID:11114902</ref> <ref>PMID:11931761</ref>	+	[https://www.uniprot.org/uniprot/RPOA_THEAQ RPOA_THEAQ]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 4xls" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4xls" 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/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 25104~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~DNA-directed RNA polymerase~~]]	+	[[Category: Synthetic construct]]
	[[Category: Thermus aquaticus]]		[[Category: Thermus aquaticus]]
-	[[Category: Thermus thermophilus jl-18]]	+	[[Category: Thermus thermophilus JL-18]]
-	[[Category: Bae, B]]	+	[[Category: Bae B]]
-	[[Category: Darst~~, S A]]~~	+	[[Category: Darst SA]]
-	~~[[Category: Bacterial transcription initiation complex]]~~	+
-	~~[[Category: Protein-dna complex]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 15:20, 16 November 2017

2017-11-16T15:20:19Z

←Older revision		Revision as of 15:20, 16 November 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 4xls is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter.==
		+	<StructureSection load='4xls' size='340' side='right' caption='[[4xls]], [[Resolution\|resolution]] 4.01Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xls]] is a 18 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104], [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus] and [http://en.wikipedia.org/wiki/Thermus_thermophilus_jl-18 Thermus thermophilus jl-18]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XLS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XLS 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">[[4xln\|4xln]], [[4xlp\|4xlp]], [[4xlq\|4xlq]], [[4xlr\|4xlr]], [[4xax\|4xax]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sigA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104]), TtJL18_0238 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=798128 Thermus thermophilus JL-18])</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=4xls FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xls OCA], [http://pdbe.org/4xls PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xls RCSB], [http://www.ebi.ac.uk/pdbsum/4xls PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xls ProSAT]</span></td></tr>
		+	</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/SIGA_THEAQ SIGA_THEAQ]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.[HAMAP-Rule:MF_00963]<ref>PMID:11114902</ref> <ref>PMID:11931761</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD.

-	~~Authors: Bae~~, B., Darst, S.A.	+	CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.,Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell EA Elife. 2015 Sep 8;4. doi: 10.7554/eLife.08505. PMID:26349034<ref>PMID:26349034</ref>

-	~~Description: Crystal structure~~ of T. ~~aquaticus transcription initiation complex with CarD containing upstream fork promoter~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Darst, S.A~~]]	+	<div class="pdbe-citations 4xls" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Atcc 25104]]
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Thermus aquaticus]]
		+	[[Category: Thermus thermophilus jl-18]]
	[[Category: Bae, B]]		[[Category: Bae, B]]
		+	[[Category: Darst, S A]]
		+	[[Category: Bacterial transcription initiation complex]]
		+	[[Category: Protein-dna complex]]
		+	[[Category: Transcription]]

OCA at 11:27, 18 February 2015

2015-02-18T11:27:38Z

←Older revision		Revision as of 11:27, 18 February 2015
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4xls is ON HOLD	+	The entry 4xls is ON HOLD until Paper Publication

	Authors: Bae, B., Darst, S.A.		Authors: Bae, B., Darst, S.A.

-	Description: Crystal structure of T.aquaticus transcription initiation complex with CarD containing upstream fork promoter.	+	Description: Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter.
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Darst, S.A]]		[[Category: Darst, S.A]]
	[[Category: Bae, B]]		[[Category: Bae, B]]

OCA: Protected "4xls" [edit=sysop:move=sysop]

2015-01-21T16:00:21Z

Protected "4xls" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:00, 21 January 2015

OCA: New page: '''Unreleased structure''' The entry 4xls is ON HOLD Authors: Bae, B., Darst, S.A. Description: Crystal structure of T.aquaticus transcription initiation complex with CarD containing u...

2015-01-21T16:00:20Z

New page: '''Unreleased structure''' The entry 4xls is ON HOLD Authors: Bae, B., Darst, S.A. Description: Crystal structure of T.aquaticus transcription initiation complex with CarD containing u...

New page

'''Unreleased structure'''

The entry 4xls is ON HOLD

Authors: Bae, B., Darst, S.A.

Description: Crystal structure of T.aquaticus transcription initiation complex with CarD containing upstream fork promoter.
[[Category: Unreleased Structures]]
[[Category: Darst, S.A]]
[[Category: Bae, B]]