6psq - Revision history

OCA at 09:27, 20 March 2024

OCA — Wed, 20 Mar 2024 09:27:12 GMT

←Older revision		Revision as of 09:27, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='6psq' size='340' side='right'caption='[[6psq]], [[Resolution\|resolution]] 3.40Å' scene=''>		<StructureSection load='6psq' size='340' side='right'caption='[[6psq]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6psq]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PSQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PSQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6psq]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PSQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PSQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=1N7:CHAPSO'>1N7</scene>~~, ~~<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]] 3.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895]), traR, ECOK12F083 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=562 "Bacillus coli" Migula 1895]), rpoA, pez, phs, sez, b3295, JW3257 ([http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoB, Z5560, ECs4910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoZ, Z5075, ECs4524 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</scene>, <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=6psq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6psq OCA], [https://pdbe.org/6psq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6psq RCSB], [https://www.ebi.ac.uk/pdbsum/6psq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6psq 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=6psq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6psq OCA], [~~http~~://pdbe.org/6psq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6psq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6psq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6psq ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/Q0P6L9_ECOLX Q0P6L9_ECOLX]] 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][SAAS:SAAS00535554] [[http://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOB_ECO57 RPOB_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOZ_ECO57 RPOZ_ECO57]] 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 (By similarity).	+	[https://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into the RNAP active site. RPo formation is a multi-step process with transient intermediates of unknown structure. We use single-particle cryoelectron microscopy to visualize seven intermediates containing Escherichia coli RNAP with the transcription factor TraR en route to forming RPo. The structures span the RPo formation pathway from initial recognition of the duplex promoter in a closed complex to the final RPo. The structures and supporting biochemical data define RNAP and promoter DNA conformational changes that delineate steps on the pathway, including previously undetected transient promoter-RNAP interactions that contribute to populating the intermediates but do not occur in RPo. Our work provides a structural basis for understanding RPo formation and its regulation, a major checkpoint in gene expression throughout evolution.	+

-	Stepwise Promoter Melting by Bacterial RNA Polymerase.,Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA Mol Cell. 2020 Mar 2. pii: S1097-2765(20)30110-6. doi:, 10.1016/j.molcel.2020.02.017. PMID:32160514<ref>PMID:32160514</ref>	+	==See Also==
-		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+	*[[Sigma factor 3D structures\|Sigma factor 3D structures]]
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6psq" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: DNA-directed RNA polymerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Campbell~~, E A~~]]	+	[[Category: Campbell EA]]
-	[[Category: Chen, J]]	+	[[Category: Chen J]]
-	[[Category: Chiu~~, C E~~]]	+	[[Category: Chiu CE]]
-	[[Category: Darst~~, S A]]~~	+	[[Category: Darst SA]]
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 07:02, 29 April 2020

OCA — Wed, 29 Apr 2020 07:02:00 GMT

←Older revision		Revision as of 07:02, 29 April 2020
Line 3:		Line 3:
	<StructureSection load='6psq' size='340' side='right'caption='[[6psq]], [[Resolution\|resolution]] 3.40Å' scene=''>		<StructureSection load='6psq' size='340' side='right'caption='[[6psq]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6psq]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PSQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PSQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6psq]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PSQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PSQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</scene>, <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=1N7:CHAPSO'>1N7</scene>, <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">rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), traR, ECOK12F083 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoA, pez, phs, sez, b3295, JW3257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoB, Z5560, ECs4910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoZ, Z5075, ECs4524 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpoD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=6psq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6psq OCA], [http://pdbe.org/6psq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6psq RCSB], [http://www.ebi.ac.uk/pdbsum/6psq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6psq 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=6psq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6psq OCA], [http://pdbe.org/6psq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6psq RCSB], [http://www.ebi.ac.uk/pdbsum/6psq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6psq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 10:13, 27 March 2020

OCA — Fri, 27 Mar 2020 10:13:00 GMT

←Older revision		Revision as of 10:13, 27 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6psq is ~~ON HOLD until Paper~~ Publication	+	==Escherichia coli RNA polymerase closed complex (TRPc) with TraR and rpsT P2 promoter==
		+	<StructureSection load='6psq' size='340' side='right'caption='[[6psq]], [[Resolution\|resolution]] 3.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6psq]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PSQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PSQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1N7:CHAPSO'>1N7</scene>, <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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6psq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6psq OCA], [http://pdbe.org/6psq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6psq RCSB], [http://www.ebi.ac.uk/pdbsum/6psq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6psq ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q0P6L9_ECOLX Q0P6L9_ECOLX]] 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][SAAS:SAAS00535554] [[http://www.uniprot.org/uniprot/RPOA_ECOLI RPOA_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit plays an important role in subunit assembly since its dimerization is the first step in the sequential assembly of subunits to form the holoenzyme.[HAMAP-Rule:MF_00059] [[http://www.uniprot.org/uniprot/RPOC_ECOLI RPOC_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322] [[http://www.uniprot.org/uniprot/RPOB_ECO57 RPOB_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOZ_ECO57 RPOZ_ECO57]] 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 (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Transcription initiation requires formation of the open promoter complex (RPo). To generate RPo, RNA polymerase (RNAP) unwinds the DNA duplex to form the transcription bubble and loads the DNA into the RNAP active site. RPo formation is a multi-step process with transient intermediates of unknown structure. We use single-particle cryoelectron microscopy to visualize seven intermediates containing Escherichia coli RNAP with the transcription factor TraR en route to forming RPo. The structures span the RPo formation pathway from initial recognition of the duplex promoter in a closed complex to the final RPo. The structures and supporting biochemical data define RNAP and promoter DNA conformational changes that delineate steps on the pathway, including previously undetected transient promoter-RNAP interactions that contribute to populating the intermediates but do not occur in RPo. Our work provides a structural basis for understanding RPo formation and its regulation, a major checkpoint in gene expression throughout evolution.

-	~~Authors~~:	+	Stepwise Promoter Melting by Bacterial RNA Polymerase.,Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA Mol Cell. 2020 Mar 2. pii: S1097-2765(20)30110-6. doi:, 10.1016/j.molcel.2020.02.017. PMID:32160514<ref>PMID:32160514</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6psq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Campbell, E A]]
		+	[[Category: Chen, J]]
		+	[[Category: Chiu, C E]]
		+	[[Category: Darst, S A]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription-dna complex]]

OCA at 05:32, 4 March 2020

OCA — Wed, 04 Mar 2020 05:32:44 GMT

←Older revision		Revision as of 05:32, 4 March 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6psq is ON HOLD	+	The entry 6psq is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 13:14, 29 January 2020

OCA — Wed, 29 Jan 2020 13:14:12 GMT

←Older revision		Revision as of 13:14, 29 January 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6psq is ON HOLD ~~until Paper Publication~~	+	The entry 6psq is ON HOLD

	Authors:		Authors:

OCA at 04:53, 23 October 2019

OCA — Wed, 23 Oct 2019 04:53:55 GMT

←Older revision		Revision as of 04:53, 23 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6psq is ON HOLD	+	The entry 6psq is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6psq" [edit=sysop:move=sysop]

OCA — Wed, 24 Jul 2019 04:31:00 GMT

Protected "6psq" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:31, 24 July 2019

OCA: New page: '''Unreleased structure''' The entry 6psq is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 24 Jul 2019 04:30:58 GMT

New page: '''Unreleased structure''' The entry 6psq is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6psq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]