6jbq - Revision history

OCA at 10:37, 27 March 2024

2024-03-27T10:37:32Z

←Older revision		Revision as of 10:37, 27 March 2024
Line 3:		Line 3:
	<SX load='6jbq' size='340' side='right' viewer='molstar' caption='[[6jbq]], [[Resolution\|resolution]] 4.02Å' scene=''>		<SX load='6jbq' size='340' side='right' viewer='molstar' caption='[[6jbq]], [[Resolution\|resolution]] 4.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jbq]] is a 9 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6JBQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jbq]] is a 9 chain structure with sequence from [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=6JBQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JBQ FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 4.02Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>rpoA, pez, phs, sez, b3295, JW3257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=83333 ECOLI]), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoZ, b3649, JW3624 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoE, sigE, b2573, JW2557 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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~~='~~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=6jbq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbq OCA], [https://pdbe.org/6jbq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jbq RCSB], [https://www.ebi.ac.uk/pdbsum/6jbq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbq 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=6jbq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbq OCA], [~~http~~://pdbe.org/6jbq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jbq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jbq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbq ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[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_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[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/RPOZ_ECOLI RPOZ_ECOLI]] 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.[HAMAP-Rule:MF_00366] [[http://www.uniprot.org/uniprot/RPOE_ECOLI RPOE_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase (RNAP) to specific initiation sites and are then released. Extracytoplasmic function (ECF) sigma-E controls the envelope stress response, responding to periplasmic protein stress, increased levels of periplasmic lipopolysaccharide (LPS) as well as heat shock and oxidative stress; it controls protein processing in the extracytoplasmic compartment. The 90 member regulon consists of the genes necessary for the synthesis and maintenance of both proteins and LPS of the outer membrane.<ref>PMID:7889935</ref> <ref>PMID:7889934</ref> <ref>PMID:2691330</ref> <ref>PMID:9159522</ref> <ref>PMID:9159523</ref> <ref>PMID:16336047</ref>	+	[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 ==~~	+
-	Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) sigma factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 A of Escherichia coli transcription initiation complex comprising sigmaE-the most-studied bacterial ECF sigma factor (Ec sigmaE-RPo), and a crystal structure at 3.1 A of Mycobacterium tuberculosis transcription initiation complex with a chimeric sigmaH/E (Mtb sigmaH/E-RPo). The structure of Ec sigmaE-RPo reveals key interactions essential for assembly of E. coli sigmaE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli sigmaE. Moreover, both structures show that the non-conserved linkers (sigma2/sigma4 linker) of the two ECF sigma factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF sigma factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such sigma2/sigma4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF sigma factors-mediated transcription initiation.	+
-		+
-	Structures and mechanism of transcription initiation by bacterial ECF factors.,Fang C, Li L, Shen L, Shi J, Wang S, Feng Y, Zhang Y Nucleic Acids Res. 2019 May 27. pii: 5498757. doi: 10.1093/nar/gkz470. PMID:31131408<ref>PMID:31131408</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6jbq" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]		*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	*[[Sigma factor 3D structures\|Sigma factor 3D structures]]		*[[Sigma factor 3D structures\|Sigma factor 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: ~~DNA~~-~~directed RNA polymerase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Fang, C L~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Zhang, Y~~]]	+	[[Category: Fang CL]]
-	[[Category: ~~Extra-cytoplasmic function sigma factor]]~~	+	[[Category: Zhang Y]]
-	~~[[Category: Rna polymerase]]~~	+
-	~~[[Category: Sigmae]]~~	+
-	~~[[Category: Transcription initiation]]~~	+
-	~~[[Category: Transcription-dna-rna complex~~]]	+

OCA at 02:05, 11 April 2020

2020-04-11T02:05:10Z

←Older revision		Revision as of 02:05, 11 April 2020
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	<SX load='6jbq' size='340' side='right' viewer='molstar' caption='[[6jbq]], [[Resolution\|resolution]] 4.02Å' scene=''>		<SX load='6jbq' size='340' side='right' viewer='molstar' caption='[[6jbq]], [[Resolution\|resolution]] 4.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jbq]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JBQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jbq]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JBQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=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">rpoA, pez, phs, sez, b3295, JW3257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoZ, b3649, JW3624 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoE, sigE, b2573, JW2557 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA, pez, phs, sez, b3295, JW3257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoZ, b3649, JW3624 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoE, sigE, b2573, JW2557 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6jbq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbq OCA], [http://pdbe.org/6jbq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jbq RCSB], [http://www.ebi.ac.uk/pdbsum/6jbq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbq 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=6jbq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbq OCA], [http://pdbe.org/6jbq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jbq RCSB], [http://www.ebi.ac.uk/pdbsum/6jbq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 22:15, 6 March 2020

2020-03-06T22:15:43Z

←Older revision		Revision as of 22:15, 6 March 2020
Line 1:		Line 1:

	==CryoEM structure of Escherichia coli sigmaE transcription initiation complex containing 5nt of RNA==		==CryoEM structure of Escherichia coli sigmaE transcription initiation complex containing 5nt of RNA==
-	<~~StructureSection~~ load='6jbq' size='340' side='right'caption='[[6jbq]], [[Resolution\|resolution]] 4.02Å' scene=''>	+	<SX load='6jbq' size='340' side='right' viewer='molstar' caption='[[6jbq]], [[Resolution\|resolution]] 4.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6jbq]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JBQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[6jbq]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JBQ FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6jbq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6jbq" 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 ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
	[[Category: Ecoli]]		[[Category: Ecoli]]

OCA at 23:05, 5 June 2019

2019-06-05T23:05:57Z

←Older revision		Revision as of 23:05, 5 June 2019
Line 3:		Line 3:
	<StructureSection load='6jbq' size='340' side='right'caption='[[6jbq]], [[Resolution\|resolution]] 4.02Å' scene=''>		<StructureSection load='6jbq' size='340' side='right'caption='[[6jbq]], [[Resolution\|resolution]] 4.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jbq]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JBQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jbq]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JBQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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"><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">rpoA, pez, phs, sez, b3295, JW3257 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoC, tabB, b3988, JW3951 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoZ, b3649, JW3624 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpoE, sigE, b2573, JW2557 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6jbq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbq OCA], [http://pdbe.org/6jbq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jbq RCSB], [http://www.ebi.ac.uk/pdbsum/6jbq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbq ProSAT]</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=6jbq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbq OCA], [http://pdbe.org/6jbq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jbq RCSB], [http://www.ebi.ac.uk/pdbsum/6jbq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbq ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[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_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[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/RPOZ_ECOLI RPOZ_ECOLI]] 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.[HAMAP-Rule:MF_00366] [[http://www.uniprot.org/uniprot/RPOE_ECOLI RPOE_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase (RNAP) to specific initiation sites and are then released. Extracytoplasmic function (ECF) sigma-E controls the envelope stress response, responding to periplasmic protein stress, increased levels of periplasmic lipopolysaccharide (LPS) as well as heat shock and oxidative stress; it controls protein processing in the extracytoplasmic compartment. The 90 member regulon consists of the genes necessary for the synthesis and maintenance of both proteins and LPS of the outer membrane.<ref>PMID:7889935</ref> <ref>PMID:7889934</ref> <ref>PMID:2691330</ref> <ref>PMID:9159522</ref> <ref>PMID:9159523</ref> <ref>PMID:16336047</ref>		[[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_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[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/RPOZ_ECOLI RPOZ_ECOLI]] 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.[HAMAP-Rule:MF_00366] [[http://www.uniprot.org/uniprot/RPOE_ECOLI RPOE_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase (RNAP) to specific initiation sites and are then released. Extracytoplasmic function (ECF) sigma-E controls the envelope stress response, responding to periplasmic protein stress, increased levels of periplasmic lipopolysaccharide (LPS) as well as heat shock and oxidative stress; it controls protein processing in the extracytoplasmic compartment. The 90 member regulon consists of the genes necessary for the synthesis and maintenance of both proteins and LPS of the outer membrane.<ref>PMID:7889935</ref> <ref>PMID:7889934</ref> <ref>PMID:2691330</ref> <ref>PMID:9159522</ref> <ref>PMID:9159523</ref> <ref>PMID:16336047</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial RNA polymerase (RNAP) forms distinct holoenzymes with extra-cytoplasmic function (ECF) sigma factors to initiate specific gene expression programs. In this study, we report a cryo-EM structure at 4.0 A of Escherichia coli transcription initiation complex comprising sigmaE-the most-studied bacterial ECF sigma factor (Ec sigmaE-RPo), and a crystal structure at 3.1 A of Mycobacterium tuberculosis transcription initiation complex with a chimeric sigmaH/E (Mtb sigmaH/E-RPo). The structure of Ec sigmaE-RPo reveals key interactions essential for assembly of E. coli sigmaE-RNAP holoenzyme and for promoter recognition and unwinding by E. coli sigmaE. Moreover, both structures show that the non-conserved linkers (sigma2/sigma4 linker) of the two ECF sigma factors are inserted into the active-center cleft and exit through the RNA-exit channel. We performed secondary-structure prediction of 27,670 ECF sigma factors and find that their non-conserved linkers probably reach into and exit from RNAP active-center cleft in a similar manner. Further biochemical results suggest that such sigma2/sigma4 linker plays an important role in RPo formation, abortive production and promoter escape during ECF sigma factors-mediated transcription initiation.
		+
		+	Structures and mechanism of transcription initiation by bacterial ECF factors.,Fang C, Li L, Shen L, Shi J, Wang S, Feng Y, Zhang Y Nucleic Acids Res. 2019 May 27. pii: 5498757. doi: 10.1093/nar/gkz470. PMID:31131408<ref>PMID:31131408</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6jbq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fang, C L]]		[[Category: Fang, C L]]

OCA at 06:12, 29 May 2019

2019-05-29T06:12:21Z

←Older revision		Revision as of 06:12, 29 May 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6jbq is ~~ON HOLD until Paper Publication~~	+	==CryoEM structure of Escherichia coli sigmaE transcription initiation complex containing 5nt of RNA==
-		+	<StructureSection load='6jbq' size='340' side='right'caption='[[6jbq]], [[Resolution\|resolution]] 4.02Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6jbq]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JBQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JBQ FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6jbq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbq OCA], [http://pdbe.org/6jbq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jbq RCSB], [http://www.ebi.ac.uk/pdbsum/6jbq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbq ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[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_ECOLI RPOB_ECOLI]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01321] [[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/RPOZ_ECOLI RPOZ_ECOLI]] 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.[HAMAP-Rule:MF_00366] [[http://www.uniprot.org/uniprot/RPOE_ECOLI RPOE_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase (RNAP) to specific initiation sites and are then released. Extracytoplasmic function (ECF) sigma-E controls the envelope stress response, responding to periplasmic protein stress, increased levels of periplasmic lipopolysaccharide (LPS) as well as heat shock and oxidative stress; it controls protein processing in the extracytoplasmic compartment. The 90 member regulon consists of the genes necessary for the synthesis and maintenance of both proteins and LPS of the outer membrane.<ref>PMID:7889935</ref> <ref>PMID:7889934</ref> <ref>PMID:2691330</ref> <ref>PMID:9159522</ref> <ref>PMID:9159523</ref> <ref>PMID:16336047</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Fang, C L]]
		+	[[Category: Zhang, Y]]
		+	[[Category: Extra-cytoplasmic function sigma factor]]
		+	[[Category: Rna polymerase]]
		+	[[Category: Sigmae]]
		+	[[Category: Transcription initiation]]
		+	[[Category: Transcription-dna-rna complex]]

OCA at 04:57, 21 February 2019

2019-02-21T04:57:22Z

←Older revision		Revision as of 04:57, 21 February 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2019-02-13T07:19:30Z

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

←Older revision

Revision as of 07:19, 13 February 2019

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

2019-02-13T07:19:28Z

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

New page

'''Unreleased structure'''

The entry 6jbq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]