6pmj - Revision history

OCA at 09:26, 20 March 2024

OCA — Wed, 20 Mar 2024 09:26:33 GMT

←Older revision		Revision as of 09:26, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='6pmj' size='340' side='right'caption='[[6pmj]], [[Resolution\|resolution]] 3.91Å' scene=''>		<StructureSection load='6pmj' size='340' side='right'caption='[[6pmj]], [[Resolution\|resolution]] 3.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pmj]] is a 9 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Eco45 Eco45~~], [~~http~~://en.wikipedia.org/wiki/~~Eco57 Eco57~~] and [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PMJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PMJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pmj]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12], [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7] and [https://en.wikipedia.org/wiki/Escherichia_coli_S88 Escherichia coli S88]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PMJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PMJ 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]] 3.91Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <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">[[6pmi\|6pmi]]</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=6pmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pmj OCA], [https://pdbe.org/6pmj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pmj RCSB], [https://www.ebi.ac.uk/pdbsum/6pmj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pmj ProSAT]</span></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">rpoA~~, Z4665, ECs4160 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57]), rpoB, ECS88_4448 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585035 ECO45]), rpoC, Z5561, ECs4911 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57]), rpoZ, ECS88_4064 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585035 ECO45]), fliA, flaD, rpoF, b1922, JW1907 ([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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6pmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pmj OCA], [~~http~~://pdbe.org/6pmj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pmj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pmj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pmj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~RPOC_ECO57 RPOC_ECO57]~~] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. ~~[[http://www.uniprot.org/uniprot/RPOB_ECO45 RPOB_ECO45]] DNA-dependent RNA polymerase catalyzes~~ the ~~transcription of DNA into RNA using~~ the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOA_ECO57 RPOA_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOZ_ECO45 RPOZ_ECO45]] 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~~. [[http://www.uniprot.org/uniprot/FLIA_ECOLI FLIA_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase~~ to ~~specific initiation sites and are then released. This sigma factor controls~~ the ~~expression of flagella-related genes~~.[HAMAP-Rule:~~MF_00962~~]~~<ref>PMID:2644646</ref> <ref>PMID:3536871</ref> <ref>PMID:7590326</ref> <ref>PMID:8866483</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 ==~~	+
-	In bacteria, sigma(28) is the flagella-specific sigma factor that targets RNA polymerase (RNAP) to control the expression of flagella-related genes involving bacterial motility and chemotaxis. However, the structural mechanism of sigma(28) -dependent promoter recognition remains uncharacterized. Here, we report cryo-EM structures of E. coli sigma(28) -dependent transcribing complexes on a complete flagella-specific promoter. These structures reveal how sigma(28) -RNAP recognizes promoter DNA through strong interactions with the -10 element, but weak contacts with the -35 element, to initiate transcription. In addition, we observed a distinct architecture in which the beta' zinc-binding domain (ZBD) of RNAP stretches out from its canonical position to interact with the upstream non-template strand. Further in vitro and in vivo assays demonstrate that this interaction has the overall effect of facilitating closed-to-open isomerization of the RNAP-promoter complex by compensating for the weak interaction between sigma4 and -35 element. This suggests that ZBD relocation may be a general mechanism employed by sigma(70) family factors to enhance transcription from promoters with weak sigma4/-35 element interactions.	+

-	Structural basis of bacterial sigma(28) -mediated transcription reveals roles of the RNA polymerase zinc-binding domain.,Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B EMBO J. 2020 Jun 2:e104389. doi: 10.15252/embj.2020104389. PMID:32484956<ref>PMID:32484956</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 6pmj" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA-directed RNA polymerase~~]]	+	[[Category: Escherichia coli]]
-	[[Category: ~~Eco45~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: ~~Eco57~~]]	+	[[Category: Escherichia coli O157:H7]]
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli S88]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Liu, B]]	+	[[Category: Liu B]]
-	[[Category: Shi, W]]	+	[[Category: Shi W]]
-	~~[[Category: Rpof]]~~	+
-	~~[[Category: Sigma28]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription initiation complex]]~~	+
-	~~[[Category: Znr domain~~]]	+

OCA at 10:36, 17 June 2020

OCA — Wed, 17 Jun 2020 10:36:59 GMT

←Older revision		Revision as of 10:36, 17 June 2020
Line 1:		Line 1:

	==Sigm28-transcription initiation complex with specific promoter at the state 2==		==Sigm28-transcription initiation complex with specific promoter at the state 2==
-	<StructureSection load='6pmj' size='340' side='right'caption='[[6pmj]]' scene=''>	+	<StructureSection load='6pmj' size='340' side='right'caption='[[6pmj]], [[Resolution\|resolution]] 3.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PMJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PMJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pmj]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco45 Eco45], [http://en.wikipedia.org/wiki/Eco57 Eco57] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PMJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PMJ FirstGlance]. <br>
-	</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=6pmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pmj OCA], [http://pdbe.org/6pmj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pmj RCSB], [http://www.ebi.ac.uk/pdbsum/6pmj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pmj ProSAT]</span></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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6pmi\|6pmi]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rpoA, Z4665, ECs4160 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57]), rpoB, ECS88_4448 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585035 ECO45]), rpoC, Z5561, ECs4911 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57]), rpoZ, ECS88_4064 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585035 ECO45]), fliA, flaD, rpoF, b1922, JW1907 ([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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6pmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pmj OCA], [http://pdbe.org/6pmj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pmj RCSB], [http://www.ebi.ac.uk/pdbsum/6pmj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pmj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RPOC_ECO57 RPOC_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOB_ECO45 RPOB_ECO45]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOA_ECO57 RPOA_ECO57]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. [[http://www.uniprot.org/uniprot/RPOZ_ECO45 RPOZ_ECO45]] 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. [[http://www.uniprot.org/uniprot/FLIA_ECOLI FLIA_ECOLI]] Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor controls the expression of flagella-related genes.[HAMAP-Rule:MF_00962]<ref>PMID:2644646</ref> <ref>PMID:3536871</ref> <ref>PMID:7590326</ref> <ref>PMID:8866483</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In bacteria, sigma(28) is the flagella-specific sigma factor that targets RNA polymerase (RNAP) to control the expression of flagella-related genes involving bacterial motility and chemotaxis. However, the structural mechanism of sigma(28) -dependent promoter recognition remains uncharacterized. Here, we report cryo-EM structures of E. coli sigma(28) -dependent transcribing complexes on a complete flagella-specific promoter. These structures reveal how sigma(28) -RNAP recognizes promoter DNA through strong interactions with the -10 element, but weak contacts with the -35 element, to initiate transcription. In addition, we observed a distinct architecture in which the beta' zinc-binding domain (ZBD) of RNAP stretches out from its canonical position to interact with the upstream non-template strand. Further in vitro and in vivo assays demonstrate that this interaction has the overall effect of facilitating closed-to-open isomerization of the RNAP-promoter complex by compensating for the weak interaction between sigma4 and -35 element. This suggests that ZBD relocation may be a general mechanism employed by sigma(70) family factors to enhance transcription from promoters with weak sigma4/-35 element interactions.
		+
		+	Structural basis of bacterial sigma(28) -mediated transcription reveals roles of the RNA polymerase zinc-binding domain.,Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B EMBO J. 2020 Jun 2:e104389. doi: 10.15252/embj.2020104389. PMID:32484956<ref>PMID:32484956</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6pmj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: DNA-directed RNA polymerase]]
		+	[[Category: Eco45]]
		+	[[Category: Eco57]]
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Liu B]]	+	[[Category: Liu, B]]
-	[[Category: Shi W]]	+	[[Category: Shi, W]]
		+	[[Category: Rpof]]
		+	[[Category: Sigma28]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription initiation complex]]
		+	[[Category: Znr domain]]

OCA at 05:27, 13 May 2020

OCA — Wed, 13 May 2020 05:27:42 GMT

←Older revision		Revision as of 05:27, 13 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6pmj ~~is ON HOLD~~	+	==Sigm28-transcription initiation complex with specific promoter at the state 2==
-		+	<StructureSection load='6pmj' size='340' side='right'caption='[[6pmj]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PMJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PMJ FirstGlance]. <br>
-	~~Description~~:	+	</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=6pmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pmj OCA], [http://pdbe.org/6pmj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pmj RCSB], [http://www.ebi.ac.uk/pdbsum/6pmj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pmj ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Liu B]]
		+	[[Category: Shi W]]

OCA at 13:49, 22 January 2020

OCA — Wed, 22 Jan 2020 13:49:11 GMT

←Older revision		Revision as of 13:49, 22 January 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

OCA at 05:10, 27 November 2019

OCA — Wed, 27 Nov 2019 05:10:34 GMT

←Older revision		Revision as of 05:10, 27 November 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 10 Jul 2019 04:16:11 GMT

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

←Older revision

Revision as of 04:16, 10 July 2019

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

OCA — Wed, 10 Jul 2019 04:16:10 GMT

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

New page

'''Unreleased structure'''

The entry 6pmj is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]