6dvb - Revision history

OCA at 14:37, 13 March 2024

2024-03-13T14:37:05Z

← Older revision		Revision as of 14:37, 13 March 2024
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	==Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) containing 5nt RNA with 5nt spacer==		==Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) containing 5nt RNA with 5nt spacer==
	<StructureSection load='6dvb' size='340' side='right' caption='[[6dvb]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='6dvb' size='340' side='right'caption='[[6dvb]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dvb]] is a 9 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dvb]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DVB FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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">X-ray diffraction, [[Resolution\|Resolution]] 3.8Å</td></tr>
	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]</b></td><td class="sblockDat">rpoA, Rv3457c, MTCY13E12.10c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU]), rpoB, Rv0667, MTCI376.08c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.~~cgi?mode=Info~~&srchmode=5&id=83332 MYCTU]), rpoC, Rv0668, MTCI376.07c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU]), rpoZ, Rv1390, MTCY21B4.07 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU]), sigL, Rv0735 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=6dvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvb OCA], [https://pdbe.org/6dvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dvb RCSB], [https://www.ebi.ac.uk/pdbsum/6dvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvb 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=6dvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvb OCA], [~~http~~://pdbe.org/6dvb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dvb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dvb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RPOC_MYCTU RPOC_MYCTU]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322]<ref>PMID:22570422</ref> [[http://www.uniprot.org/uniprot/RPOB_MYCTU RPOB_MYCTU]] 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_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> [[http://www.uniprot.org/uniprot/RPOZ_MYCTU RPOZ_MYCTU]] 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.<ref>PMID:22570422</ref> [[http://www.uniprot.org/uniprot/SIGL_MYCTU SIGL_MYCTU]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. Extracytoplasmic function (ECF) sigma factors are held in an inactive form by an anti-sigma factor until released by regulated intramembrane proteolysis. Over-expression of SigL induces 19-28 genes including polyketide synthases, secreted and membrane proteins. Might play a minor role in regulating SigB.<ref>PMID:16199577</ref> <ref>PMID:16552079</ref>		[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 ==~~
	Extracytoplasmic (ECF) sigma factors, the largest class of alternative sigma factors, are related to primary sigma factors, but have simpler structures, comprising only two of six conserved functional modules in primary sigma factors: region 2 (sigmaR2) and region 4 (sigmaR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF sigma factor sigma(L), and promoter DNA. The structures show that sigmaR2 and sigmaR4 of the ECF sigma factor occupy the same sites on RNAP as in primary sigma factors, show that the connector between sigmaR2 and sigmaR4 of the ECF sigma factor-although shorter and unrelated in sequence-follows the same path through RNAP as in primary sigma factors, and show that the ECF sigma factor uses the same strategy to bind and unwind promoter DNA as primary sigma factors. The results define protein-protein and protein-DNA interactions involved in ECF-sigma-factor-dependent transcription initiation.

	Structural basis of ECF-sigma-factor-dependent transcription initiation.,Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K, Ebright RH Nat Commun. 2019 Feb 12;10(1):710. doi: 10.1038/s41467-019-08443-3. PMID:30755604<ref>PMID:30755604</ref>		==See Also==
			*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~		*[[Sigma factor 3D structures\|Sigma factor 3D structures]]
	~~</div>~~
	~~<div class="pdbe-citations 6dvb" style="background-color:#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~DNA-directed RNA polymerase~~]]		[[Category: Large Structures]]
	[[Category: ~~Myctu~~]]		[[Category: Mycobacterium tuberculosis H37Rv]]
	[[Category: Das, K]]		[[Category: Das K]]
	[[Category: Ebright~~, R H~~]]		[[Category: Ebright RH]]
	[[Category: Feng, Y]]		[[Category: Feng Y]]
	[[Category: Lin, W]]		[[Category: Lin W]]
	~~[[Category: Ecf sigma factor]]~~
	~~[[Category: Mycobacterium tuberculosis]]~~
	~~[[Category: Rna polymerase]]~~
	~~[[Category: Transferase]]~~
	~~[[Category: Transferase-dna-rna complex~~]]

OCA at 15:56, 27 February 2019

2019-02-27T15:56:43Z

← Older revision		Revision as of 15:56, 27 February 2019
Line 3:		Line 3:
	<StructureSection load='6dvb' size='340' side='right' caption='[[6dvb]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='6dvb' size='340' side='right' caption='[[6dvb]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dvb]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dvb]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA, Rv3457c, MTCY13E12.10c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU]), rpoB, Rv0667, MTCI376.08c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU]), rpoC, Rv0668, MTCI376.07c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU]), rpoZ, Rv1390, MTCY21B4.07 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU]), sigL, Rv0735 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=6dvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvb OCA], [http://pdbe.org/6dvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dvb RCSB], [http://www.ebi.ac.uk/pdbsum/6dvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvb 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=6dvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dvb OCA], [http://pdbe.org/6dvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dvb RCSB], [http://www.ebi.ac.uk/pdbsum/6dvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dvb ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RPOC_MYCTU RPOC_MYCTU]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322]<ref>PMID:22570422</ref> [[http://www.uniprot.org/uniprot/RPOB_MYCTU RPOB_MYCTU]] 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_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> [[http://www.uniprot.org/uniprot/RPOZ_MYCTU RPOZ_MYCTU]] 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.<ref>PMID:22570422</ref> [[http://www.uniprot.org/uniprot/SIGL_MYCTU SIGL_MYCTU]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. Extracytoplasmic function (ECF) sigma factors are held in an inactive form by an anti-sigma factor until released by regulated intramembrane proteolysis. Over-expression of SigL induces 19-28 genes including polyketide synthases, secreted and membrane proteins. Might play a minor role in regulating SigB.<ref>PMID:16199577</ref> <ref>PMID:16552079</ref>		[[http://www.uniprot.org/uniprot/RPOC_MYCTU RPOC_MYCTU]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322]<ref>PMID:22570422</ref> [[http://www.uniprot.org/uniprot/RPOB_MYCTU RPOB_MYCTU]] 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_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> [[http://www.uniprot.org/uniprot/RPOZ_MYCTU RPOZ_MYCTU]] 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.<ref>PMID:22570422</ref> [[http://www.uniprot.org/uniprot/SIGL_MYCTU SIGL_MYCTU]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. Extracytoplasmic function (ECF) sigma factors are held in an inactive form by an anti-sigma factor until released by regulated intramembrane proteolysis. Over-expression of SigL induces 19-28 genes including polyketide synthases, secreted and membrane proteins. Might play a minor role in regulating SigB.<ref>PMID:16199577</ref> <ref>PMID:16552079</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Extracytoplasmic (ECF) sigma factors, the largest class of alternative sigma factors, are related to primary sigma factors, but have simpler structures, comprising only two of six conserved functional modules in primary sigma factors: region 2 (sigmaR2) and region 4 (sigmaR4). Here, we report crystal structures of transcription initiation complexes containing Mycobacterium tuberculosis RNA polymerase (RNAP), M. tuberculosis ECF sigma factor sigma(L), and promoter DNA. The structures show that sigmaR2 and sigmaR4 of the ECF sigma factor occupy the same sites on RNAP as in primary sigma factors, show that the connector between sigmaR2 and sigmaR4 of the ECF sigma factor-although shorter and unrelated in sequence-follows the same path through RNAP as in primary sigma factors, and show that the ECF sigma factor uses the same strategy to bind and unwind promoter DNA as primary sigma factors. The results define protein-protein and protein-DNA interactions involved in ECF-sigma-factor-dependent transcription initiation.

			Structural basis of ECF-sigma-factor-dependent transcription initiation.,Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K, Ebright RH Nat Commun. 2019 Feb 12;10(1):710. doi: 10.1038/s41467-019-08443-3. PMID:30755604<ref>PMID:30755604</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6dvb" 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: Myctu]]
	[[Category: Das, K]]		[[Category: Das, K]]
	[[Category: Ebright, R H]]		[[Category: Ebright, R H]]

OCA at 06:38, 21 February 2019

2019-02-21T06:38:59Z

@@ Line 1: / Line 1: @@
-The entry 6dvb is ON HOLD  until Paper Publication
+==Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) containing 5nt RNA with 5nt spacer==
+<StructureSection load='6dvb' size='340' side='right' caption='[[6dvb]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6dvb]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DVB FirstGlance]. <br>
-Description:
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>

OCA at 08:40, 5 September 2018

2018-09-05T08:40:33Z

← Older revision		Revision as of 08:40, 5 September 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6dvb is ON HOLD		The entry 6dvb is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 04:03, 11 July 2018

2018-07-11T04:03:27Z

← Older revision		Revision as of 04:03, 11 July 2018
Line 3:		Line 3:
	The entry 6dvb is ON HOLD		The entry 6dvb is ON HOLD

	Authors: ~~Lin, W., Das, K., Feng, Y., Ebright, R.H.~~		Authors:

	Description: ~~Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) containing 5nt RNA with 5nt spacer~~		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	~~[[Category: Lin, W]]~~
	~~[[Category: Das, K]]~~
	~~[[Category: Ebright, R.H]]~~
	~~[[Category: Feng, Y]]~~

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

2018-07-04T05:44:24Z

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

← Older revision	Revision as of 05:44, 4 July 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6dvb is ON HOLD Authors: Lin, W., Das, K., Feng, Y., Ebright, R.H. Description: Crystal structure of Mycobacterium tuberculosis transcription initi...

2018-07-04T05:44:23Z

New page: '''Unreleased structure''' The entry 6dvb is ON HOLD Authors: Lin, W., Das, K., Feng, Y., Ebright, R.H. Description: Crystal structure of Mycobacterium tuberculosis transcription initi...

New page

'''Unreleased structure'''

The entry 6dvb is ON HOLD

Authors: Lin, W., Das, K., Feng, Y., Ebright, R.H.

Description: Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) containing 5nt RNA with 5nt spacer
[[Category: Unreleased Structures]]
[[Category: Lin, W]]
[[Category: Das, K]]
[[Category: Ebright, R.H]]
[[Category: Feng, Y]]