5ond - Revision history

OCA at 16:55, 13 December 2023

OCA — Wed, 13 Dec 2023 16:55:26 GMT

←Older revision		Revision as of 16:55, 13 December 2023
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	<StructureSection load='5ond' size='340' side='right'caption='[[5ond]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5ond' size='340' side='right'caption='[[5ond]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ond]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OND OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5OND FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ond]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OND OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OND 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=5ond FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ond OCA], [~~http~~://pdbe.org/5ond PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ond RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ond PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ond ProSAT]</span></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]] 2.1Å</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=5ond FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ond OCA], [https://pdbe.org/5ond PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ond RCSB], [https://www.ebi.ac.uk/pdbsum/5ond PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ond ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RFAH_ECOLI RFAH_ECOLI]] Enhances distal genes transcription elongation in a specialized subset of operons that encode extracytoplasmic components. RfaH is recruited into a multi-component RNA polymerase complex by the ops element, which is a short conserved DNA sequence located downstream of the main promoter of these operons. Once bound, RfaH suppresses pausing and inhibits Rho-dependent and intrinsic termination at a subset of sites. Termination signals are bypassed, which allows complete synthesis of long RNA chains. Enhances expression of several operons involved in synthesis of lipopolysaccharides, exopolysaccharides, hemolysin, and sex factor. Also negatively controls expression and surface presentation of AG43 and possibly another AG43-independent factor that mediates cell-cell interactions and biofilm formation.<ref>PMID:1584020</ref> <ref>PMID:8606157</ref> <ref>PMID:8951819</ref> <ref>PMID:9171395</ref> <ref>PMID:9426123</ref> <ref>PMID:10660066</ref> <ref>PMID:12007406</ref> <ref>PMID:11983161</ref> <ref>PMID:16452414</ref>	+	[https://www.uniprot.org/uniprot/RFAH_ECOLI RFAH_ECOLI] Enhances distal genes transcription elongation in a specialized subset of operons that encode extracytoplasmic components. RfaH is recruited into a multi-component RNA polymerase complex by the ops element, which is a short conserved DNA sequence located downstream of the main promoter of these operons. Once bound, RfaH suppresses pausing and inhibits Rho-dependent and intrinsic termination at a subset of sites. Termination signals are bypassed, which allows complete synthesis of long RNA chains. Enhances expression of several operons involved in synthesis of lipopolysaccharides, exopolysaccharides, hemolysin, and sex factor. Also negatively controls expression and surface presentation of AG43 and possibly another AG43-independent factor that mediates cell-cell interactions and biofilm formation.<ref>PMID:1584020</ref> <ref>PMID:8606157</ref> <ref>PMID:8951819</ref> <ref>PMID:9171395</ref> <ref>PMID:9426123</ref> <ref>PMID:10660066</ref> <ref>PMID:12007406</ref> <ref>PMID:11983161</ref> <ref>PMID:16452414</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Artsimovitch, I]]	+	[[Category: Artsimovitch I]]
-	[[Category: Knauer~~, S H~~]]	+	[[Category: Knauer SH]]
-	[[Category: Roesch, P]]	+	[[Category: Roesch P]]
-	[[Category: Zuber~~, P K]]~~	+	[[Category: Zuber PK]]
-	~~[[Category: Binding of single stranded dna]]~~	+
-	~~[[Category: Operon-specific transcription factor]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transformer protein]]~~	+
-	~~[[Category: Translation activation~~]]	+

OCA at 07:29, 2 September 2020

OCA — Wed, 02 Sep 2020 07:29:30 GMT

←Older revision		Revision as of 07:29, 2 September 2020
Line 1:		Line 1:

	==RfaH from Escherichia coli in complex with ops DNA==		==RfaH from Escherichia coli in complex with ops DNA==
-	<StructureSection load='5ond' size='340' side='right' caption='[[5ond]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5ond' size='340' side='right'caption='[[5ond]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ond]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OND OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OND FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ond]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OND OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OND FirstGlance]. <br>
-	</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=5ond FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ond OCA], [http://pdbe.org/5ond PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ond RCSB], [http://www.ebi.ac.uk/pdbsum/5ond PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ond ProSAT]</span></td></tr>	+	</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=5ond FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ond OCA], [http://pdbe.org/5ond PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ond RCSB], [http://www.ebi.ac.uk/pdbsum/5ond PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ond ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5ond" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ond" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcriptional activator 3D structures\|Transcriptional activator 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Artsimovitch, I]]		[[Category: Artsimovitch, I]]
	[[Category: Knauer, S H]]		[[Category: Knauer, S H]]

OCA at 05:48, 6 June 2018

OCA — Wed, 06 Jun 2018 05:48:30 GMT

←Older revision		Revision as of 05:48, 6 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ond is ~~ON HOLD~~	+	==RfaH from Escherichia coli in complex with ops DNA==
		+	<StructureSection load='5ond' size='340' side='right' caption='[[5ond]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ond]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OND OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OND FirstGlance]. <br>
		+	</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=5ond FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ond OCA], [http://pdbe.org/5ond PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ond RCSB], [http://www.ebi.ac.uk/pdbsum/5ond PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ond ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RFAH_ECOLI RFAH_ECOLI]] Enhances distal genes transcription elongation in a specialized subset of operons that encode extracytoplasmic components. RfaH is recruited into a multi-component RNA polymerase complex by the ops element, which is a short conserved DNA sequence located downstream of the main promoter of these operons. Once bound, RfaH suppresses pausing and inhibits Rho-dependent and intrinsic termination at a subset of sites. Termination signals are bypassed, which allows complete synthesis of long RNA chains. Enhances expression of several operons involved in synthesis of lipopolysaccharides, exopolysaccharides, hemolysin, and sex factor. Also negatively controls expression and surface presentation of AG43 and possibly another AG43-independent factor that mediates cell-cell interactions and biofilm formation.<ref>PMID:1584020</ref> <ref>PMID:8606157</ref> <ref>PMID:8951819</ref> <ref>PMID:9171395</ref> <ref>PMID:9426123</ref> <ref>PMID:10660066</ref> <ref>PMID:12007406</ref> <ref>PMID:11983161</ref> <ref>PMID:16452414</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RfaH, a transcription regulator of the universally conserved NusG/Spt5 family, utilizes a unique mode of recruitment to elongating RNA polymerase to activate virulence genes. RfaH function depends critically on an ops sequence, an exemplar of a consensus pause, in the non-template DNA strand of the transcription bubble. We used structural and functional analyses to elucidate the role of ops in RfaH recruitment. Our results demonstrate that ops induces pausing to facilitate RfaH binding and establishes direct contacts with RfaH. Strikingly, the non-template DNA forms a hairpin in the RfaH:ops complex structure, flipping out a conserved T residue that is specifically recognized by RfaH. Molecular modeling and genetic evidence support the notion that ops hairpin is required for RfaH recruitment. We argue that both the sequence and the structure of the non-template strand are read out by transcription factors, expanding the repertoire of transcriptional regulators in all domains of life.

-	~~Authors: Zuber, P.K~~., ~~Artsimovitch~~, I., ~~Roesch~~, P., Knauer~~, S~~.H.	+	The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand.,Zuber PK, Artsimovitch I, NandyMazumdar M, Liu Z, Nedialkov Y, Schweimer K, Rosch P, Knauer SH Elife. 2018 May 9;7. pii: 36349. doi: 10.7554/eLife.36349. PMID:29741479<ref>PMID:29741479</ref>

-	~~Description: RfaH from Escherichia coli in complex with ops DNA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category: Knauer~~, S.~~H]]~~	+	<div class="pdbe-citations 5ond" style="background-color:#fffaf0;"></div>
-	~~[[Category~~: ~~Roesch, P]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Artsimovitch, I]]		[[Category: Artsimovitch, I]]
-	[[Category: Zuber, P.K]]	+	[[Category: Knauer, S H]]
		+	[[Category: Roesch, P]]
		+	[[Category: Zuber, P K]]
		+	[[Category: Binding of single stranded dna]]
		+	[[Category: Operon-specific transcription factor]]
		+	[[Category: Transcription]]
		+	[[Category: Transformer protein]]
		+	[[Category: Translation activation]]

OCA: Protected "5ond" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:37:12 GMT

Protected "5ond" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:37, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ond is ON HOLD Authors: Zuber, P.K., Artsimovitch, I., Roesch, P., Knauer, S.H. Description: RfaH from Escherichia coli in complex with ops DNA [[...

OCA — Wed, 27 Sep 2017 12:37:11 GMT

New page: '''Unreleased structure''' The entry 5ond is ON HOLD Authors: Zuber, P.K., Artsimovitch, I., Roesch, P., Knauer, S.H. Description: RfaH from Escherichia coli in complex with ops DNA [[...

New page

'''Unreleased structure'''

The entry 5ond is ON HOLD

Authors: Zuber, P.K., Artsimovitch, I., Roesch, P., Knauer, S.H.

Description: RfaH from Escherichia coli in complex with ops DNA
[[Category: Unreleased Structures]]
[[Category: Knauer, S.H]]
[[Category: Roesch, P]]
[[Category: Artsimovitch, I]]
[[Category: Zuber, P.K]]