OCA at 16:53, 29 November 2023

OCA — Wed, 29 Nov 2023 16:53:30 GMT

←Older revision		Revision as of 16:53, 29 November 2023
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-	====	+	==Thermus thermophilus RNA polymerase transcription initiation complex containing a template-strand purine at position TSS-2, UpA RNA primer and CMPcPP==
-	<StructureSection load='7eh0' size='340' side='right'caption='[[7eh0]]' scene=''>	+	<StructureSection load='7eh0' size='340' side='right'caption='[[7eh0]], [[Resolution\|resolution]] 2.81Å' 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'>[[7eh0]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8] 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=7EH0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EH0 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=7eh0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eh0 OCA], [https://pdbe.org/7eh0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eh0 RCSB], [https://www.ebi.ac.uk/pdbsum/7eh0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eh0 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]] 2.808Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2TM:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]CYTIDINE'>2TM</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=7eh0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eh0 OCA], [https://pdbe.org/7eh0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eh0 RCSB], [https://www.ebi.ac.uk/pdbsum/7eh0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eh0 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RPOB_THET8 RPOB_THET8] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Chemical modifications of RNA 5'-ends enable "epitranscriptomic" regulation, influencing multiple aspects of RNA fate. In transcription initiation, a large inventory of substrates compete with nucleoside triphosphates for use as initiating entities, providing an ab initio mechanism for altering the RNA 5'-end. In Escherichia coli cells, RNAs with a 5'-end hydroxyl are generated by use of dinucleotide RNAs as primers for transcription initiation, "primer-dependent initiation." Here, we use massively systematic transcript end readout (MASTER) to detect and quantify RNA 5'-ends generated by primer-dependent initiation for approximately 4(10) ( approximately 1,000,000) promoter sequences in E. coli The results show primer-dependent initiation in E. coli involves any of the 16 possible dinucleotide primers and depends on promoter sequences in, upstream, and downstream of the primer binding site. The results yield a consensus sequence for primer-dependent initiation, Y(TSS-2)N(TSS-1)N(TSS)W(TSS+1), where TSS is the transcription start site, N(TSS-1)N(TSS) is the primer binding site, Y is pyrimidine, and W is A or T. Biochemical and structure-determination studies show that the base pair (nontemplate-strand base:template-strand base) immediately upstream of the primer binding site (Y:R(TSS-2), where R is purine) exerts its effect through the base on the DNA template strand (R(TSS-2)) through interchain base stacking with the RNA primer. Results from analysis of a large set of natural, chromosomally encoded Ecoli promoters support the conclusions from MASTER. Our findings provide a mechanistic and structural description of how TSS-region sequence hard-codes not only the TSS position but also the potential for epitranscriptomic regulation through primer-dependent transcription initiation.
		+
		+	Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli.,Skalenko KS, Li L, Zhang Y, Vvedenskaya IO, Winkelman JT, Cope AL, Taylor DM, Shah P, Ebright RH, Kinney JB, Zhang Y, Nickels BE Proc Natl Acad Sci U S A. 2021 Jul 6;118(27):e2106388118. doi: , 10.1073/pnas.2106388118. PMID:34187896<ref>PMID:34187896</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7eh0" 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: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Synthetic construct]]
		+	[[Category: Thermus thermophilus HB8]]
		+	[[Category: Li L]]
		+	[[Category: Zhang Y]]

OCA at 09:52, 14 July 2021

OCA — Wed, 14 Jul 2021 09:52:26 GMT

←Older revision		Revision as of 09:52, 14 July 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7eh0 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7eh0' size='340' side='right'caption='[[7eh0]]' 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=7eh0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eh0 OCA], [https://pdbe.org/7eh0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eh0 RCSB], [https://www.ebi.ac.uk/pdbsum/7eh0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eh0 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 05:34, 14 April 2021

OCA — Wed, 14 Apr 2021 05:34:25 GMT

←Older revision		Revision as of 05:34, 14 April 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7eh0 is ON HOLD	+	The entry 7eh0 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7eh0" [edit=sysop:move=sysop]

OCA — Wed, 07 Apr 2021 04:30:04 GMT

Protected "7eh0" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:30, 7 April 2021

OCA: New page: '''Unreleased structure''' The entry 7eh0 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 07 Apr 2021 04:30:03 GMT

New page: '''Unreleased structure''' The entry 7eh0 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7eh0 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7eh0 - Revision history

OCA at 16:53, 29 November 2023

OCA at 09:52, 14 July 2021

OCA at 05:34, 14 April 2021

OCA: Protected "7eh0" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 7eh0 is ON HOLD Authors: Description: Category: Unreleased Structures