6f6w - Revision history

OCA at 00:40, 11 April 2020

OCA — Sat, 11 Apr 2020 00:40:55 GMT

←Older revision		Revision as of 00:40, 11 April 2020
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	<SX load='6f6w' size='340' side='right' viewer='molstar' caption='[[6f6w]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='6f6w' size='340' side='right' viewer='molstar' caption='[[6f6w]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6f6w]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6W OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6F6W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6f6w]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6W OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6F6W 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6eyd\|6eyd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6eyd\|6eyd]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA, MSMEG_1524, MSMEI_1488 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoB, MSMEG_1367, MSMEI_1328 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoC, MSMEG_1368, MSMEI_1329 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoZ, MSMEG_3053, MSMEI_2977 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA, MSMEG_1524, MSMEI_1488 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoB, MSMEG_1367, MSMEI_1328 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoC, MSMEG_1368, MSMEI_1329 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoZ, MSMEG_3053, MSMEI_2977 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</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=6f6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f6w OCA], [http://pdbe.org/6f6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f6w RCSB], [http://www.ebi.ac.uk/pdbsum/6f6w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f6w 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=6f6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f6w OCA], [http://pdbe.org/6f6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f6w RCSB], [http://www.ebi.ac.uk/pdbsum/6f6w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f6w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 21:13, 6 March 2020

OCA — Fri, 06 Mar 2020 21:13:20 GMT

←Older revision		Revision as of 21:13, 6 March 2020
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	==Structure of Mycobacterium smegmatis RNA polymerase core==		==Structure of Mycobacterium smegmatis RNA polymerase core==
-	<~~StructureSection~~ load='6f6w' size='340' side='right'caption='[[6f6w]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<SX load='6f6w' size='340' side='right' viewer='molstar' caption='[[6f6w]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6f6w]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F6W FirstGlance]. <br>		<table><tr><td colspan='2'>[[6f6w]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F6W FirstGlance]. <br>
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 6f6w" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6f6w" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase 3D structures\|RNA polymerase 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 06:45, 31 July 2019

OCA — Wed, 31 Jul 2019 06:45:56 GMT

←Older revision		Revision as of 06:45, 31 July 2019
Line 1:		Line 1:

	==Structure of Mycobacterium smegmatis RNA polymerase core==		==Structure of Mycobacterium smegmatis RNA polymerase core==
-	<StructureSection load='6f6w' size='340' side='right' caption='[[6f6w]], [[Resolution\|resolution]] 3.80Å' scene=''>	+	<StructureSection load='6f6w' size='340' side='right'caption='[[6f6w]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6f6w]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F6W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6f6w]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycs2 Mycs2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F6W 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6eyd\|6eyd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6eyd\|6eyd]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA, MSMEG_1524, MSMEI_1488 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoB, MSMEG_1367, MSMEI_1328 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoC, MSMEG_1368, MSMEI_1329 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2]), rpoZ, MSMEG_3053, MSMEI_2977 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246196 MYCS2])</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=6f6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f6w OCA], [http://pdbe.org/6f6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f6w RCSB], [http://www.ebi.ac.uk/pdbsum/6f6w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f6w 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=6f6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f6w OCA], [http://pdbe.org/6f6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f6w RCSB], [http://www.ebi.ac.uk/pdbsum/6f6w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f6w ProSAT]</span></td></tr>
Line 25:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: DNA-directed RNA polymerase]]		[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Mycs2]]
	[[Category: Barvik, I]]		[[Category: Barvik, I]]
	[[Category: Kouba, T]]		[[Category: Kouba, T]]

OCA at 08:26, 19 December 2018

OCA — Wed, 19 Dec 2018 08:26:14 GMT

←Older revision		Revision as of 08:26, 19 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6f6w is ~~ON HOLD~~	+	==Structure of Mycobacterium smegmatis RNA polymerase core==
		+	<StructureSection load='6f6w' size='340' side='right' caption='[[6f6w]], [[Resolution\|resolution]] 3.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6f6w]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F6W 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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6eyd\|6eyd]]</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=6f6w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f6w OCA], [http://pdbe.org/6f6w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f6w RCSB], [http://www.ebi.ac.uk/pdbsum/6f6w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f6w ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPOZ_MYCS2 RPOZ_MYCS2]] 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]<ref>PMID:19926651</ref> [[http://www.uniprot.org/uniprot/RPOA_MYCS2 RPOA_MYCS2]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_00059]<ref>PMID:19926651</ref> [[http://www.uniprot.org/uniprot/RPOC_MYCS2 RPOC_MYCS2]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[HAMAP-Rule:MF_01322]<ref>PMID:19926651</ref> [[http://www.uniprot.org/uniprot/RPOB_MYCS2 RPOB_MYCS2]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. This subunit often mutates to generate rifampicin (Rif) resistance. Interaction with RbpA partially restores Rif-inhibited transcription; once the subunit is Rif-resistant however RbpA no longer stimulates transcription.[HAMAP-Rule:MF_01321]<ref>PMID:19926651</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial RNA polymerase (RNAP) is essential for gene expression and as such is a valid drug target. Hence, it is imperative to know its structure and dynamics. Here, we present two so far unreported forms of Mycobacteium smegmatis RNAP: core, and holoenzyme containing sigma(A) but no other factors. Each form was detected by cryo-EM in two major conformations. Comparisons of these structures with known structures of other RNAPs reveal a high degree of conformational flexibility of the mycobacterial enzyme, and confirm that region 1.1 of sigma(A) is directed into the primary channel of RNAP. Taken together, the presented study illuminates the conformational changes of unrestrained mycobacterial RNAP.IMPORTANCE We describe here 3D structures of core and holoenzyme forms of mycobacterial RNA polymerase (RNAP) solved by cryo-EM. These structures fill the so far empty spots in the gallery of the pivotal forms of mycobacterial RNAP and illuminate the extent of conformational dynamics of this enzyme. The presented findings may facilitate future designs of antimycobacterial drugs targeting RNAP.

-	~~Authors~~:	+	The Core and Holoenzyme forms of RNA Polymerase from Mycobacterium smegmatis.,Kouba T, Pospisil J, Hnilicova J, Sanderova H, Barvik I, Krasny L J Bacteriol. 2018 Nov 26. pii: JB.00583-18. doi: 10.1128/JB.00583-18. PMID:30478083<ref>PMID:30478083</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6f6w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Barvik, I]]
		+	[[Category: Kouba, T]]
		+	[[Category: Krasny, L]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription sigma]]

OCA at 18:27, 2 December 2018

OCA — Sun, 02 Dec 2018 18:27:00 GMT

←Older revision		Revision as of 18:27, 2 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6f6w is ON HOLD ~~until Paper Publication~~	+	The entry 6f6w is ON HOLD

	Authors:		Authors:

OCA at 12:35, 11 April 2018

OCA — Wed, 11 Apr 2018 12:35:40 GMT

←Older revision		Revision as of 12:35, 11 April 2018
Line 3:		Line 3:
	The entry 6f6w is ON HOLD until Paper Publication		The entry 6f6w is ON HOLD until Paper Publication

-	Authors: ~~Kouba, T., Barvik, I., Krasny, L.~~	+	Authors:

-	Description: ~~Structure of Mycobacterium smegmatis RNA polymerase core~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Barvik, I]]
-	[[Category: Krasny, L]]
-	[[Category: Kouba, T]]

OCA at 05:50, 17 January 2018

OCA — Wed, 17 Jan 2018 05:50:00 GMT

←Older revision		Revision as of 05:50, 17 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6f6w is ON HOLD	+	The entry 6f6w is ON HOLD until Paper Publication

	Authors: Kouba, T., Barvik, I., Krasny, L.		Authors: Kouba, T., Barvik, I., Krasny, L.

OCA: Protected "6f6w" [edit=sysop:move=sysop]

OCA — Wed, 13 Dec 2017 06:03:18 GMT

Protected "6f6w" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:03, 13 December 2017

OCA: New page: '''Unreleased structure''' The entry 6f6w is ON HOLD Authors: Kouba, T., Barvik, I., Krasny, L. Description: Structure of Mycobacterium smegmatis RNA polymerase core [[Category: Unrele...

OCA — Wed, 13 Dec 2017 06:03:16 GMT

New page: '''Unreleased structure''' The entry 6f6w is ON HOLD Authors: Kouba, T., Barvik, I., Krasny, L. Description: Structure of Mycobacterium smegmatis RNA polymerase core [[Category: Unrele...

New page

'''Unreleased structure'''

The entry 6f6w is ON HOLD

Authors: Kouba, T., Barvik, I., Krasny, L.

Description: Structure of Mycobacterium smegmatis RNA polymerase core
[[Category: Unreleased Structures]]
[[Category: Barvik, I]]
[[Category: Krasny, L]]
[[Category: Kouba, T]]