4v2s - Revision history

OCA at 10:39, 10 January 2024

OCA — Wed, 10 Jan 2024 10:39:40 GMT

←Older revision		Revision as of 10:39, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4v2s]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V2S FirstGlance]. <br>		<table><tr><td colspan='2'>[[4v2s]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V2S FirstGlance]. <br>
-	</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=4v2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2s OCA], [https://pdbe.org/4v2s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v2s RCSB], [https://www.ebi.ac.uk/pdbsum/4v2s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v2s 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]] 3.48Å</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=4v2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2s OCA], [https://pdbe.org/4v2s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v2s RCSB], [https://www.ebi.ac.uk/pdbsum/4v2s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v2s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:

	==See Also==		==See Also==
-	*[[Protein Hfq\|Protein Hfq]]	+	*[[Protein Hfq 3D structures\|Protein Hfq 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:00, 29 March 2023

OCA — Wed, 29 Mar 2023 08:00:14 GMT

←Older revision		Revision as of 08:00, 29 March 2023
Line 1:		Line 1:

	==Crystal structure of Hfq in complex with the sRNA RydC==		==Crystal structure of Hfq in complex with the sRNA RydC==
-	<StructureSection load='4v2s' size='340' side='right' caption='[[4v2s]], [[Resolution\|resolution]] 3.48Å' scene=''>	+	<StructureSection load='4v2s' size='340' side='right'caption='[[4v2s]], [[Resolution\|resolution]] 3.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4v2s]] is a 7 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4V2S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4v2s]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V2S 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=4v2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2s OCA], [~~http~~://pdbe.org/4v2s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4v2s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4v2s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4v2s ProSAT]</span></td></tr>	+	</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=4v2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2s OCA], [https://pdbe.org/4v2s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v2s RCSB], [https://www.ebi.ac.uk/pdbsum/4v2s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v2s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HFQ_ECOLI HFQ_ECOLI]] RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Involved in the regulation of stress responses mediated by the sigma factors RpoS, sigma-E and sigma-32. Binds with high specificity to tRNAs. In vitro, stimulates synthesis of long tails by poly(A) polymerase I. Required for RNA phage Qbeta replication.<ref>PMID:805130</ref> <ref>PMID:10677490</ref> <ref>PMID:11222598</ref> <ref>PMID:17158661</ref> <ref>PMID:19909729</ref> Seems to play a role in persister cell formation; upon overexpression decreases persister cell formation while deletion increases persister formation.<ref>PMID:805130</ref> <ref>PMID:10677490</ref> <ref>PMID:11222598</ref> <ref>PMID:17158661</ref> <ref>PMID:19909729</ref>	+	[https://www.uniprot.org/uniprot/HFQ_ECOLI HFQ_ECOLI] RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Involved in the regulation of stress responses mediated by the sigma factors RpoS, sigma-E and sigma-32. Binds with high specificity to tRNAs. In vitro, stimulates synthesis of long tails by poly(A) polymerase I. Required for RNA phage Qbeta replication.<ref>PMID:805130</ref> <ref>PMID:10677490</ref> <ref>PMID:11222598</ref> <ref>PMID:17158661</ref> <ref>PMID:19909729</ref> Seems to play a role in persister cell formation; upon overexpression decreases persister cell formation while deletion increases persister formation.<ref>PMID:805130</ref> <ref>PMID:10677490</ref> <ref>PMID:11222598</ref> <ref>PMID:17158661</ref> <ref>PMID:19909729</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 4v2s" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4v2s" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Protein Hfq\|Protein Hfq]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Bandyra,~~ K J]]	+	[[Category: Large Structures]]
-	[[Category: ~~Bruce, H A~~]]	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-	[[Category: ~~Dimastrogiovanni, D~~]]	+	[[Category: Bandyra KJ]]
-	[[Category: ~~Frohlich, K S~~]]	+	[[Category: Bruce HA]]
-	[[Category: ~~Hohensee, S~~]]	+	[[Category: Dimastrogiovanni D]]
-	[[Category: ~~Luisi, B F~~]]	+	[[Category: Frohlich KS]]
-	[[Category: ~~Vogel, J~~]]	+	[[Category: Hohensee S]]
-	[[Category: ~~Natively unstructured protein~~]]	+	[[Category: Luisi BF]]
-	[[Category: ~~Protein-rna recognition~~]]	+	[[Category: Vogel J]]
-	[[Category: ~~Rna binding protein-rna complex~~]]	+

OCA at 15:47, 27 February 2019

OCA — Wed, 27 Feb 2019 15:47:07 GMT

←Older revision		Revision as of 15:47, 27 February 2019
Line 1:		Line 1:
		+
	==Crystal structure of Hfq in complex with the sRNA RydC==		==Crystal structure of Hfq in complex with the sRNA RydC==
	<StructureSection load='4v2s' size='340' side='right' caption='[[4v2s]], [[Resolution\|resolution]] 3.48Å' scene=''>		<StructureSection load='4v2s' size='340' side='right' caption='[[4v2s]], [[Resolution\|resolution]] 3.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4v2s]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V2S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4v2s]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V2S 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=4v2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2s OCA], [http://pdbe.org/4v2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v2s RCSB], [http://www.ebi.ac.uk/pdbsum/4v2s PDBsum]</span></td></tr>	+	</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=4v2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2s OCA], [http://pdbe.org/4v2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v2s RCSB], [http://www.ebi.ac.uk/pdbsum/4v2s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v2s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Bandyra, K J]]		[[Category: Bandyra, K J]]
	[[Category: Bruce, H A]]		[[Category: Bruce, H A]]

OCA at 07:03, 16 December 2015

OCA — Wed, 16 Dec 2015 07:03:42 GMT

←Older revision		Revision as of 07:03, 16 December 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4v2s]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V2S FirstGlance]. <br>		<table><tr><td colspan='2'>[[4v2s]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V2S 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=4v2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4v2s RCSB], [http://www.ebi.ac.uk/pdbsum/4v2s PDBsum]</span></td></tr>	+	</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=4v2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2s OCA], [http://pdbe.org/4v2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v2s RCSB], [http://www.ebi.ac.uk/pdbsum/4v2s PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 15:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4v2s" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:29, 14 January 2015

OCA — Wed, 14 Jan 2015 13:29:25 GMT

←Older revision		Revision as of 13:29, 14 January 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of Hfq in complex with the sRNA RydC==
		+	<StructureSection load='4v2s' size='340' side='right' caption='[[4v2s]], [[Resolution\|resolution]] 3.48Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4v2s]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V2S 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=4v2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4v2s RCSB], [http://www.ebi.ac.uk/pdbsum/4v2s PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HFQ_ECOLI HFQ_ECOLI]] RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Involved in the regulation of stress responses mediated by the sigma factors RpoS, sigma-E and sigma-32. Binds with high specificity to tRNAs. In vitro, stimulates synthesis of long tails by poly(A) polymerase I. Required for RNA phage Qbeta replication.<ref>PMID:805130</ref> <ref>PMID:10677490</ref> <ref>PMID:11222598</ref> <ref>PMID:17158661</ref> <ref>PMID:19909729</ref> Seems to play a role in persister cell formation; upon overexpression decreases persister cell formation while deletion increases persister formation.<ref>PMID:805130</ref> <ref>PMID:10677490</ref> <ref>PMID:11222598</ref> <ref>PMID:17158661</ref> <ref>PMID:19909729</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial small RNAs (sRNAs) are key elements of regulatory networks that modulate gene expression. The sRNA RydC of Salmonella sp. and Escherichia coli is an example of this class of riboregulators. Like many other sRNAs, RydC bears a 'seed' region that recognises specific transcripts through base-pairing, and its activities are facilitated by the RNA chaperone Hfq. The crystal structure of RydC in complex with E. coli Hfq at 3.48 A resolution illuminates how the protein interacts with and presents the sRNA for target recognition. Consolidating the protein-RNA complex is a host of distributed interactions mediated by the natively unstructured termini of Hfq. Based on the structure and other data, we propose a model for a dynamic effector complex comprising Hfq, small RNA, and the cognate mRNA target.

-	~~The entry 4v2s is ON HOLD until Paper Publication~~	+	Recognition of the small regulatory RNA RydC by the bacterial Hfq protein.,Dimastrogiovanni D, Frohlich KS, Bandyra KJ, Bruce HA, Hohensee S, Vogel J, Luisi BF Elife. 2014 Dec 31;3. doi: 10.7554/eLife.05375. PMID:25551292<ref>PMID:25551292</ref>

-	~~Authors: Dimastrogiovanni~~, ~~D., Frohlich, K~~.S.~~, Bruce, H~~.~~A.,~~ Bandyra, K.J~~., Hohensee, S., Vogel, J., Luisi, B.F.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of Hfq in complex with the sRNA RydC~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: ~~Luisi~~, ~~B.F~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Bandyra, K J]]
		+	[[Category: Bruce, H A]]
		+	[[Category: Dimastrogiovanni, D]]
		+	[[Category: Frohlich, K S]]
	[[Category: Hohensee, S]]		[[Category: Hohensee, S]]
-	[[Category: ~~Bruce~~, ~~H.A~~]]	+	[[Category: Luisi, B F]]
	[[Category: Vogel, J]]		[[Category: Vogel, J]]
-	[[Category: ~~Dimastrogiovanni, D~~]]	+	[[Category: Natively unstructured protein]]
-	[[Category: ~~Bandyra, K.J~~]]	+	[[Category: Protein-rna recognition]]
-	[[Category: ~~Frohlich, K.S~~]]	+	[[Category: Rna binding protein-rna complex]]

OCA at 19:02, 24 December 2014

OCA — Wed, 24 Dec 2014 19:02:15 GMT

←Older revision		Revision as of 19:02, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of Hfq in complex with the sRNA RydC		Description: Crystal structure of Hfq in complex with the sRNA RydC
		+	[[Category: Unreleased Structures]]
		+	[[Category: Luisi, B.F]]
		+	[[Category: Hohensee, S]]
		+	[[Category: Bruce, H.A]]
		+	[[Category: Vogel, J]]
		+	[[Category: Dimastrogiovanni, D]]
		+	[[Category: Bandyra, K.J]]
		+	[[Category: Frohlich, K.S]]

OCA at 07:53, 5 November 2014

OCA — Wed, 05 Nov 2014 07:53:44 GMT

←Older revision		Revision as of 07:53, 5 November 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4v2s is ON HOLD	+	The entry 4v2s is ON HOLD until Paper Publication

	Authors: Dimastrogiovanni, D., Frohlich, K.S., Bruce, H.A., Bandyra, K.J., Hohensee, S., Vogel, J., Luisi, B.F.		Authors: Dimastrogiovanni, D., Frohlich, K.S., Bruce, H.A., Bandyra, K.J., Hohensee, S., Vogel, J., Luisi, B.F.

	Description: Crystal structure of Hfq in complex with the sRNA RydC		Description: Crystal structure of Hfq in complex with the sRNA RydC

OCA: Protected "4v2s" [edit=sysop:move=sysop]

OCA — Wed, 22 Oct 2014 10:04:20 GMT

Protected "4v2s" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:04, 22 October 2014

OCA: New page: '''Unreleased structure''' The entry 4v2s is ON HOLD Authors: Dimastrogiovanni, D., Frohlich, K.S., Bruce, H.A., Bandyra, K.J., Hohensee, S., Vogel, J., Luisi, B.F. Description: Crysta...

OCA — Wed, 22 Oct 2014 10:04:18 GMT

New page: '''Unreleased structure''' The entry 4v2s is ON HOLD Authors: Dimastrogiovanni, D., Frohlich, K.S., Bruce, H.A., Bandyra, K.J., Hohensee, S., Vogel, J., Luisi, B.F. Description: Crysta...

New page

'''Unreleased structure'''

The entry 4v2s is ON HOLD

Authors: Dimastrogiovanni, D., Frohlich, K.S., Bruce, H.A., Bandyra, K.J., Hohensee, S., Vogel, J., Luisi, B.F.

Description: Crystal structure of Hfq in complex with the sRNA RydC