OCA at 19:41, 29 May 2024

2024-05-29T19:41:47Z

← Older revision		Revision as of 19:41, 29 May 2024
Line 1:		Line 1:

	====		==Escherichia coli sigma 70-dependent paused transcription elongation complex==
	<StructureSection load='7n4e' size='340' side='right'caption='[[7n4e]]' scene=''>		<StructureSection load='7n4e' size='340' side='right'caption='[[7n4e]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>		<table><tr><td colspan='2'>[[7n4e]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] 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=7N4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N4E FirstGlance]. <br>
	</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=7n4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n4e OCA], [https://pdbe.org/7n4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n4e RCSB], [https://www.ebi.ac.uk/pdbsum/7n4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n4e ProSAT]</span></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]] 3.8Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7n4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n4e OCA], [https://pdbe.org/7n4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n4e RCSB], [https://www.ebi.ac.uk/pdbsum/7n4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n4e ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[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 ==
			In sigma-dependent transcriptional pausing, the transcription initiation factor sigma, translocating with RNA polymerase (RNAP), makes sequence-specific protein-DNA interactions with a promoter-like sequence element in the transcribed region, inducing pausing. It has been proposed that, in sigma-dependent pausing, the RNAP active center can access off-pathway "backtracked" states that are substrates for the transcript-cleavage factors of the Gre family and on-pathway "scrunched" states that mediate pause escape. Here, using site-specific protein-DNA photocrosslinking to define positions of the RNAP trailing and leading edges and of sigma relative to DNA at the lambdaPR' promoter, we show directly that sigma-dependent pausing in the absence of GreB in vitro predominantly involves a state backtracked by 2-4 bp, and sigma-dependent pausing in the presence of GreB in vitro and in vivo predominantly involves a state scrunched by 2-3 bp. Analogous experiments with a library of 47 ( approximately 16,000) transcribed-region sequences show that the state scrunched by 2-3 bp-and only that state-is associated with the consensus sequence, T-3N-2Y-1G+1, (where -1 corresponds to the position of the RNA 3' end), which is identical to the consensus for pausing in initial transcription and which is related to the consensus for pausing in transcription elongation. Experiments with heteroduplex templates show that sequence information at position T-3 resides in the DNA nontemplate strand. A cryoelectron microscopy structure of a complex engaged in sigma-dependent pausing reveals positions of DNA scrunching on the DNA nontemplate and template strands and suggests that position T-3 of the consensus sequence exerts its effects by facilitating scrunching.

			Structural and mechanistic basis of sigma-dependent transcriptional pausing.,Pukhrambam C, Molodtsov V, Kooshkbaghi M, Tareen A, Vu H, Skalenko KS, Su M, Yin Z, Winkelman JT, Kinney JB, Ebright RH, Nickels BE Proc Natl Acad Sci U S A. 2022 Jun 7;119(23):e2201301119. doi: , 10.1073/pnas.2201301119. Epub 2022 Jun 2. PMID:35653571<ref>PMID:35653571</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7n4e" 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/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Z-disk~~]]		[[Category: Synthetic construct]]
			[[Category: Ebright RH]]
			[[Category: Molodtsov V]]
			[[Category: Su M]]

OCA at 05:09, 15 June 2022

2022-06-15T05:09:57Z

← Older revision		Revision as of 05:09, 15 June 2022
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 7n4e is ~~ON HOLD until Paper Publication~~		====
			<StructureSection load='7n4e' size='340' side='right'caption='[[7n4e]]' scene=''>
	~~Authors:~~		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
	~~Description~~:		</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=7n4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n4e OCA], [https://pdbe.org/7n4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n4e RCSB], [https://www.ebi.ac.uk/pdbsum/7n4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n4e ProSAT]</span></td></tr>
	[[Category: ~~Unreleased Structures~~]]		</table>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Z-disk]]

OCA at 08:46, 7 July 2021

2021-07-07T08:46:29Z

← Older revision		Revision as of 08:46, 7 July 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7n4e is ON HOLD		The entry 7n4e is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7n4e" [edit=sysop:move=sysop]

2021-06-09T11:10:55Z

Protected "7n4e" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:10, 9 June 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7n4e is ON HOLD Authors: Description: Category: Unreleased Structures

2021-06-09T11:10:54Z

New page: '''Unreleased structure''' The entry 7n4e is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7n4e is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7n4e - Revision history

OCA at 19:41, 29 May 2024

OCA at 05:09, 15 June 2022

OCA at 08:46, 7 July 2021

OCA: Protected "7n4e" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7n4e is ON HOLD Authors: Description: Category: Unreleased Structures