6uu1 - Revision history

OCA at 07:58, 11 October 2023

2023-10-11T07:58:21Z

←Older revision		Revision as of 07:58, 11 October 2023
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-	====	+	==E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP ("Fresh" crystal soaked with CTP, GTP, and ddTTP for 30 minutes)==
-	<StructureSection load='6uu1' size='340' side='right'caption='[[6uu1]]' scene=''>	+	<StructureSection load='6uu1' size='340' side='right'caption='[[6uu1]], [[Resolution\|resolution]] 4.10Å' 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'>[[6uu1]] 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=6UU1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UU1 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=6uu1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uu1 OCA], [https://pdbe.org/6uu1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uu1 RCSB], [https://www.ebi.ac.uk/pdbsum/6uu1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uu1 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]] 4.097Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2DT:3-DEOXYTHYMIDINE-5-MONOPHOSPHATE'>2DT</scene>, <scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=6uu1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uu1 OCA], [https://pdbe.org/6uu1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uu1 RCSB], [https://www.ebi.ac.uk/pdbsum/6uu1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uu1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A377D9Q8_ECOLX A0A377D9Q8_ECOLX] [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 6uu1" 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 10:16, 13 April 2022

2022-04-13T10:16:41Z

←Older revision		Revision as of 10:16, 13 April 2022
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	<StructureSection load='6uu1' size='340' side='right'caption='[[6uu1]]' scene=''>		<StructureSection load='6uu1' size='340' side='right'caption='[[6uu1]]' 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'>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>
-	</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=6uu1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uu1 OCA], [~~http~~://pdbe.org/6uu1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6uu1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6uu1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6uu1 ProSAT]</span></td></tr>	+	</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=6uu1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uu1 OCA], [https://pdbe.org/6uu1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6uu1 RCSB], [https://www.ebi.ac.uk/pdbsum/6uu1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6uu1 ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 11:15, 26 August 2020

2020-08-26T11:15:47Z

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

-	~~The entry~~ 6uu1 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6uu1' size='340' side='right'caption='[[6uu1]]' 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 4-nt RNA and a CTP (~~""~~Fresh~~"" ~~crystal soaked with CTP~~, ~~GTP~~, ~~and ddTTP 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=6uu1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6uu1 OCA], [http://pdbe.org/6uu1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6uu1 RCSB], [http://www.ebi.ac.uk/pdbsum/6uu1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6uu1 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

2020-08-19T04:28:31Z

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

-	The entry 6uu1 is ON HOLD	+	The entry 6uu1 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 4-nt RNA and a CTP (""Fresh"" crystal soaked with CTP, GTP, and ddTTP for 30 minutes)		Description: E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP (""Fresh"" crystal soaked with CTP, GTP, and ddTTP 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 "6uu1" [edit=sysop:move=sysop]

2019-11-06T05:24:00Z

Protected "6uu1" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:24, 6 November 2019

OCA: New page: '''Unreleased structure''' The entry 6uu1 is ON HOLD Authors: Zuo, Y., De, S., Steitz, T.A. Description: E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP (""F...

2019-11-06T05:23:58Z

New page: '''Unreleased structure''' The entry 6uu1 is ON HOLD Authors: Zuo, Y., De, S., Steitz, T.A. Description: E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP (""F...

New page

'''Unreleased structure'''

The entry 6uu1 is ON HOLD

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

Description: E. coli sigma-S transcription initiation complex with a 4-nt RNA and a CTP (""Fresh"" crystal soaked with CTP, GTP, and ddTTP for 30 minutes)
[[Category: Unreleased Structures]]
[[Category: Steitz, T.A]]
[[Category: Zuo, Y]]
[[Category: De, S]]