6uu5 - Revision history

OCA at 07:58, 11 October 2023

OCA — Wed, 11 Oct 2023 07:58:26 GMT

←Older revision		Revision as of 07:58, 11 October 2023
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-	====	+	==E. coli sigma-S transcription initiation complex with a 6-nt RNA ("Old" crystal soaked with GTP, UTP, CTP, and dinucleotide GpA for 30 minutes)==
-	<StructureSection load='6uu5' size='340' side='right'caption='[[6uu5]]' scene=''>	+	<StructureSection load='6uu5' size='340' side='right'caption='[[6uu5]], [[Resolution\|resolution]] 5.40Å' 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 [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6uu5]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] 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=6UU5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UU5 FirstGlance]. <br>
-	</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=6uu5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uu5 OCA], [~~http~~://pdbe.org/6uu5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6uu5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6uu5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6uu5 ProSAT]</span></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]] 5.403Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DPO:DIPHOSPHATE'>DPO</scene>, <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=6uu5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uu5 OCA], [https://pdbe.org/6uu5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uu5 RCSB], [https://www.ebi.ac.uk/pdbsum/6uu5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uu5 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://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]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In bacteria, the dissociable sigma subunit of the RNA polymerase (RNAP) is responsible for initiating RNA synthesis from specific DNA sites. As nascent RNA grows, downstream DNA unwinds and is pulled into the RNAP, causing stress accumulation and initiation complex destabilization. Processive transcription elongation requires at least partial separation of the sigma factor from the RNAP core enzyme. Here, we present a series of transcription complexes captured between the early initiation and elongation phases via in-crystal RNA synthesis and cleavage. Crystal structures of these complexes indicate that stress accumulation during transcription initiation is not due to clashing of the growing nascent RNA with the sigma(3.2) loop, but results from scrunching of the template strand DNA that is contained inside the RNAP by the sigma(3) domain. Our results shed light on how scrunching of template-strand DNA drives both abortive initiation and sigma-RNAP core separation to transition transcription from initiation to elongation.
		+
		+	Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation.,Zuo Y, De S, Feng Y, Steitz TA iScience. 2020 Aug 11;23(9):101445. doi: 10.1016/j.isci.2020.101445. PMID:32829286<ref>PMID:32829286</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6uu5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Sigma factor 3D structures\|Sigma factor 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
		+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Synthetic construct]]
		+	[[Category: De S]]
		+	[[Category: Steitz TA]]
		+	[[Category: Zuo Y]]

OCA at 11:15, 26 August 2020

OCA — Wed, 26 Aug 2020 11:15:52 GMT

←Older revision		Revision as of 11:15, 26 August 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6uu5 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6uu5' size='340' side='right'caption='[[6uu5]]' scene=''>
-	~~Authors~~: ~~Zuo, Y~~.~~, De, S~~.~~, Steitz, T~~.A.	+	== 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 [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: E. ~~coli sigma-S transcription initiation complex with a 6-nt RNA (~~""~~Old~~"" ~~crystal soaked with GTP~~, ~~UTP~~, ~~CTP~~, ~~and dinucleotide GpA for 30 minutes)~~	+	</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=6uu5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uu5 OCA], [http://pdbe.org/6uu5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uu5 RCSB], [http://www.ebi.ac.uk/pdbsum/6uu5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uu5 ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[~~[Category~~: ~~De, S~~]]	+	__TOC__
-	[[Category: ~~Steitz, T.A~~]]	+	</StructureSection>
-	[[Category: ~~Zuo, Y~~]]	+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 04:28, 19 August 2020

OCA — Wed, 19 Aug 2020 04:28:40 GMT

←Older revision		Revision as of 04:28, 19 August 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6uu5 is ON HOLD	+	The entry 6uu5 is ON HOLD until Paper Publication

	Authors: Zuo, Y., De, S., Steitz, T.A.		Authors: Zuo, Y., De, S., Steitz, T.A.
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	Description: E. coli sigma-S transcription initiation complex with a 6-nt RNA (""Old"" crystal soaked with GTP, UTP, CTP, and dinucleotide GpA for 30 minutes)		Description: E. coli sigma-S transcription initiation complex with a 6-nt RNA (""Old"" crystal soaked with GTP, UTP, CTP, and dinucleotide GpA for 30 minutes)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: De, S]]
	[[Category: Steitz, T.A]]		[[Category: Steitz, T.A]]
	[[Category: Zuo, Y]]		[[Category: Zuo, Y]]
-	[[Category: De, S]]

OCA: Protected "6uu5" [edit=sysop:move=sysop]

OCA — Wed, 06 Nov 2019 05:24:16 GMT

Protected "6uu5" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:24, 6 November 2019

OCA: New page: '''Unreleased structure''' The entry 6uu5 is ON HOLD Authors: Zuo, Y., De, S., Steitz, T.A. Description: E. coli sigma-S transcription initiation complex with a 6-nt RNA (""Old"" cryst...

OCA — Wed, 06 Nov 2019 05:24:14 GMT

New page: '''Unreleased structure''' The entry 6uu5 is ON HOLD Authors: Zuo, Y., De, S., Steitz, T.A. Description: E. coli sigma-S transcription initiation complex with a 6-nt RNA (""Old"" cryst...

New page

'''Unreleased structure'''

The entry 6uu5 is ON HOLD

Authors: Zuo, Y., De, S., Steitz, T.A.

Description: E. coli sigma-S transcription initiation complex with a 6-nt RNA (""Old"" crystal soaked with GTP, UTP, CTP, and dinucleotide GpA for 30 minutes)
[[Category: Unreleased Structures]]
[[Category: Steitz, T.A]]
[[Category: Zuo, Y]]
[[Category: De, S]]