6m7j - Revision history

OCA at 14:41, 13 March 2024

OCA — Wed, 13 Mar 2024 14:41:32 GMT

←Older revision		Revision as of 14:41, 13 March 2024
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	<SX load='6m7j' size='340' side='right' viewer='molstar' caption='[[6m7j]], [[Resolution\|resolution]] 4.40Å' scene=''>		<SX load='6m7j' size='340' side='right' viewer='molstar' caption='[[6m7j]], [[Resolution\|resolution]] 4.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m7j]] is a 9 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M7J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6M7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m7j]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] 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=6M7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6M7J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C0L:methyl+[(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-~~dihydro~~-2H-pyran-6-yl}hex-1-en-1-yl]carbamate'>C0L</scene>, <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]] 4.4Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoB, SAMEA2682864_01701 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoZ, ERS007672_03979, ERS007703_04032, ERS007720_04749, ERS027652_00548, ERS027654_02543, ERS027656_03959, ERS124361_02246 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), sigA, mysA, rpoD, rpoV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rbpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C0L:methyl+[(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-d+ihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate'>C0L</scene>, <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=6m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m7j OCA], [https://pdbe.org/6m7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6m7j RCSB], [https://www.ebi.ac.uk/pdbsum/6m7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6m7j 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=6m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m7j OCA], [~~http~~://pdbe.org/6m7j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6m7j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6m7j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6m7j ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~RBPA_MYCTO RBPA_MYCTO]] Binds to RNA polymerase (RNAP), stimulating transcription from principal, but not alternative sigma factor promoters. [[http://www.uniprot.org/uniprot/RPOC_MYCTA RPOC_MYCTA]~~] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/V9Z879_MYCTX V9Z879_MYCTX]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [[http://www.uniprot.org/uniprot/RPOA_MYCTA RPOA_MYCTA]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/A0A0T9N9K3_MYCTX A0A0T9N9K3_MYCTX]] 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~~][SAAS:SAAS00298387] [[http://www.uniprot.org/uniprot/SIGA_MYCTO SIGA_MYCTO]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.[HAMAP-Rule:MF_00963]	+	[https://www.uniprot.org/uniprot/RPOA_MYCTU RPOA_MYCTU] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059]<ref>PMID:22570422</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	A key regulated step of transcription is promoter melting by RNA polymerase (RNAP) to form the open promoter complex(1-3). To generate the open complex, the conserved catalytic core of the RNAP combines with initiation factors to locate promoter DNA, unwind 12-14 base pairs of the DNA duplex and load the template-strand DNA into the RNAP active site. Formation of the open complex is a multi-step process during which transient intermediates of unknown structure are formed(4-6). Here we present cryo-electron microscopy structures of bacterial RNAP-promoter DNA complexes, including structures of partially melted intermediates. The structures show that late steps of promoter melting occur within the RNAP cleft, delineate key roles for fork-loop 2 and switch 2-universal structural features of RNAP-in restricting access of DNA to the RNAP active site, and explain why clamp opening is required to allow entry of single-stranded template DNA into the active site. The key roles of fork-loop 2 and switch 2 suggest a common mechanism for late steps in promoter DNA opening to enable gene expression across all domains of life.	+
-		+
-	Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding.,Boyaci H, Chen J, Jansen R, Darst SA, Campbell EA Nature. 2019 Jan;565(7739):382-385. doi: 10.1038/s41586-018-0840-5. Epub 2019 Jan, 9. PMID:30626968<ref>PMID:~~30626968~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6m7j" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 27:		Line 17:
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: DNA-directed RNA polymerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Campbell, E A~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Chen, J]]~~	+	[[Category: Synthetic construct]]
-	~~[[Category: Darst, S A~~]]	+	[[Category: Boyaci Selcuk H]]
-	[[Category: Selcuk, H ~~Boyaci~~]]	+	[[Category: Campbell EA]]
-	[[Category: ~~Closed clamp~~]]	+	[[Category: Chen J]]
-	[[Category: ~~Initiation~~]]	+	[[Category: Darst SA]]
-	[[Category: ~~Open promoter complex]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription bubble]]~~	+
-	~~[[Category: Transcription-dna complex~~]]	+

OCA at 02:39, 11 April 2020

OCA — Sat, 11 Apr 2020 02:39:45 GMT

←Older revision		Revision as of 02:39, 11 April 2020
Line 3:		Line 3:
	<SX load='6m7j' size='340' side='right' viewer='molstar' caption='[[6m7j]], [[Resolution\|resolution]] 4.40Å' scene=''>		<SX load='6m7j' size='340' side='right' viewer='molstar' caption='[[6m7j]], [[Resolution\|resolution]] 4.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6m7j]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M7J OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6M7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6m7j]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M7J OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6M7J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0L:methyl+[(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate'>C0L</scene>, <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=C0L:methyl+[(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate'>C0L</scene>, <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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoB, SAMEA2682864_01701 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoZ, ERS007672_03979, ERS007703_04032, ERS007720_04749, ERS027652_00548, ERS027654_02543, ERS027656_03959, ERS124361_02246 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), sigA, mysA, rpoD, rpoV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rbpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoB, SAMEA2682864_01701 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoZ, ERS007672_03979, ERS007703_04032, ERS007720_04749, ERS027652_00548, ERS027654_02543, ERS027656_03959, ERS124361_02246 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), sigA, mysA, rpoD, rpoV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rbpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=6m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m7j OCA], [http://pdbe.org/6m7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m7j RCSB], [http://www.ebi.ac.uk/pdbsum/6m7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m7j 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=6m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m7j OCA], [http://pdbe.org/6m7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m7j RCSB], [http://www.ebi.ac.uk/pdbsum/6m7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m7j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 22:31, 6 March 2020

OCA — Fri, 06 Mar 2020 22:31:36 GMT

←Older revision		Revision as of 22:31, 6 March 2020
Line 1:		Line 1:

	==Mycobacterium tuberculosis RNAP with RbpA/us fork and Corallopyronin==		==Mycobacterium tuberculosis RNAP with RbpA/us fork and Corallopyronin==
-	<~~StructureSection~~ load='6m7j' size='340' side='right'caption='[[6m7j]], [[Resolution\|resolution]] 4.40Å' scene=''>	+	<SX load='6m7j' size='340' side='right' viewer='molstar' caption='[[6m7j]], [[Resolution\|resolution]] 4.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6m7j]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M7J FirstGlance]. <br>		<table><tr><td colspan='2'>[[6m7j]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M7J FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6m7j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6m7j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[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: Large Structures]]		[[Category: Large Structures]]

OCA at 10:49, 18 December 2019

OCA — Wed, 18 Dec 2019 10:49:43 GMT

←Older revision		Revision as of 10:49, 18 December 2019
Line 1:		Line 1:

	==Mycobacterium tuberculosis RNAP with RbpA/us fork and Corallopyronin==		==Mycobacterium tuberculosis RNAP with RbpA/us fork and Corallopyronin==
-	<StructureSection load='6m7j' size='340' side='right' caption='[[6m7j]], [[Resolution\|resolution]] 4.40Å' scene=''>	+	<StructureSection load='6m7j' size='340' side='right'caption='[[6m7j]], [[Resolution\|resolution]] 4.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6m7j]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M7J FirstGlance]. <br>		<table><tr><td colspan='2'>[[6m7j]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M7J FirstGlance]. <br>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
	[[Category: Campbell, E A]]		[[Category: Campbell, E A]]
	[[Category: Chen, J]]		[[Category: Chen, J]]

OCA at 09:32, 30 January 2019

OCA — Wed, 30 Jan 2019 09:32:17 GMT

←Older revision		Revision as of 09:32, 30 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6m7j is ~~ON HOLD until Paper~~ Publication	+	==Mycobacterium tuberculosis RNAP with RbpA/us fork and Corallopyronin==
		+	<StructureSection load='6m7j' size='340' side='right' caption='[[6m7j]], [[Resolution\|resolution]] 4.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6m7j]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6M7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6M7J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C0L:methyl+[(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate'>C0L</scene>, <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 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoB, SAMEA2682864_01701 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rpoZ, ERS007672_03979, ERS007703_04032, ERS007720_04749, ERS027652_00548, ERS027654_02543, ERS027656_03959, ERS124361_02246 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), sigA, mysA, rpoD, rpoV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884]), rbpA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=6m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6m7j OCA], [http://pdbe.org/6m7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6m7j RCSB], [http://www.ebi.ac.uk/pdbsum/6m7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6m7j ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RBPA_MYCTO RBPA_MYCTO]] Binds to RNA polymerase (RNAP), stimulating transcription from principal, but not alternative sigma factor promoters. [[http://www.uniprot.org/uniprot/RPOC_MYCTA RPOC_MYCTA]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/V9Z879_MYCTX V9Z879_MYCTX]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [[http://www.uniprot.org/uniprot/RPOA_MYCTA RPOA_MYCTA]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/A0A0T9N9K3_MYCTX A0A0T9N9K3_MYCTX]] 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][SAAS:SAAS00298387] [[http://www.uniprot.org/uniprot/SIGA_MYCTO SIGA_MYCTO]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.[HAMAP-Rule:MF_00963]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A key regulated step of transcription is promoter melting by RNA polymerase (RNAP) to form the open promoter complex(1-3). To generate the open complex, the conserved catalytic core of the RNAP combines with initiation factors to locate promoter DNA, unwind 12-14 base pairs of the DNA duplex and load the template-strand DNA into the RNAP active site. Formation of the open complex is a multi-step process during which transient intermediates of unknown structure are formed(4-6). Here we present cryo-electron microscopy structures of bacterial RNAP-promoter DNA complexes, including structures of partially melted intermediates. The structures show that late steps of promoter melting occur within the RNAP cleft, delineate key roles for fork-loop 2 and switch 2-universal structural features of RNAP-in restricting access of DNA to the RNAP active site, and explain why clamp opening is required to allow entry of single-stranded template DNA into the active site. The key roles of fork-loop 2 and switch 2 suggest a common mechanism for late steps in promoter DNA opening to enable gene expression across all domains of life.

-	~~Authors~~:	+	Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding.,Boyaci H, Chen J, Jansen R, Darst SA, Campbell EA Nature. 2019 Jan;565(7739):382-385. doi: 10.1038/s41586-018-0840-5. Epub 2019 Jan, 9. PMID:30626968<ref>PMID:30626968</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6m7j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Campbell, E A]]
		+	[[Category: Chen, J]]
		+	[[Category: Darst, S A]]
		+	[[Category: Selcuk, H Boyaci]]
		+	[[Category: Closed clamp]]
		+	[[Category: Initiation]]
		+	[[Category: Open promoter complex]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription bubble]]
		+	[[Category: Transcription-dna complex]]

OCA at 05:25, 31 October 2018

OCA — Wed, 31 Oct 2018 05:25:32 GMT

←Older revision		Revision as of 05:25, 31 October 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6m7j is ON HOLD	+	The entry 6m7j is ON HOLD until Paper Publication

-	Authors: ~~Darst, S.A., Campbell, E.A., Boyaci Selcuk, H., Chen, J.~~	+	Authors:

-	Description: ~~Mycobacterium tuberculosis RNAP with RbpA/us fork and Corallopyronin~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Boyaci Selcuk, H]]
-	[[Category: Chen, J]]
-	[[Category: Campbell, E.A]]
-	[[Category: Darst, S.A]]

OCA: Protected "6m7j" [edit=sysop:move=sysop]

OCA — Wed, 29 Aug 2018 06:03:29 GMT

Protected "6m7j" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:03, 29 August 2018

OCA: New page: '''Unreleased structure''' The entry 6m7j is ON HOLD Authors: Darst, S.A., Campbell, E.A., Boyaci Selcuk, H., Chen, J. Description: Mycobacterium tuberculosis RNAP with RbpA/us fork an...

OCA — Wed, 29 Aug 2018 06:03:27 GMT

New page: '''Unreleased structure''' The entry 6m7j is ON HOLD Authors: Darst, S.A., Campbell, E.A., Boyaci Selcuk, H., Chen, J. Description: Mycobacterium tuberculosis RNAP with RbpA/us fork an...

New page

'''Unreleased structure'''

The entry 6m7j is ON HOLD

Authors: Darst, S.A., Campbell, E.A., Boyaci Selcuk, H., Chen, J.

Description: Mycobacterium tuberculosis RNAP with RbpA/us fork and Corallopyronin
[[Category: Unreleased Structures]]
[[Category: Boyaci Selcuk, H]]
[[Category: Chen, J]]
[[Category: Campbell, E.A]]
[[Category: Darst, S.A]]