4qvd - Revision history

OCA at 15:10, 8 November 2023

OCA — Wed, 08 Nov 2023 15:10:28 GMT

←Older revision		Revision as of 15:10, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qvd]] is a 7 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=4QVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QVD FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qvd]] is a 7 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=4QVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QVD 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=4qvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qvd OCA], [https://pdbe.org/4qvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qvd RCSB], [https://www.ebi.ac.uk/pdbsum/4qvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qvd 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]] 1.972Å</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=4qvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qvd OCA], [https://pdbe.org/4qvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qvd RCSB], [https://www.ebi.ac.uk/pdbsum/4qvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qvd 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 13:54, 22 February 2023

OCA — Wed, 22 Feb 2023 13:54:11 GMT

←Older revision		Revision as of 13:54, 22 February 2023
Line 3:		Line 3:
	<StructureSection load='4qvd' size='340' side='right'caption='[[4qvd]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='4qvd' size='340' side='right'caption='[[4qvd]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qvd]] is a 7 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QVD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4QVD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qvd]] is a 7 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=4QVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QVD FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qvc\|4qvc]]</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=4qvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qvd OCA], [https://pdbe.org/4qvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qvd RCSB], [https://www.ebi.ac.uk/pdbsum/4qvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qvd ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hfq ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4qvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qvd OCA], [~~http~~://pdbe.org/4qvd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4qvd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4qvd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4qvd ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/C1IFD2_ECOLX C1IFD2_ECOLX]] 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. Also binds with high specificity to tRNAs.[HAMAP-Rule:MF_00436]	+	[https://www.uniprot.org/uniprot/C1IFD2_ECOLX C1IFD2_ECOLX] 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. Also binds with high specificity to tRNAs.[HAMAP-Rule:MF_00436]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 4qvd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4qvd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Protein Hfq\|Protein Hfq]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gong~~, Q G~~]]	+	[[Category: Gong QG]]
-	[[Category: Li~~, F D~~]]	+	[[Category: Li FD]]
-	[[Category: Shi~~, Y Y~~]]	+	[[Category: Shi YY]]
-	[[Category: Wang~~, L J~~]]	+	[[Category: Wang LJ]]
-	[[Category: Wang~~, W W~~]]	+	[[Category: Wang WW]]
-	[[Category: Wu~~, J H]]~~	+	[[Category: Wu JH]]
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna binding protein-rna complex]]~~	+
-	~~[[Category: Rna chaperone]]~~	+
-	~~[[Category: Sm fold~~]]	+

OCA at 09:18, 24 April 2019

OCA — Wed, 24 Apr 2019 09:18:05 GMT

←Older revision		Revision as of 09:18, 24 April 2019
Line 1:		Line 1:

	==E.coli Hfq in complex with RNA Ads==		==E.coli Hfq in complex with RNA Ads==
-	<StructureSection load='4qvd' size='340' side='right' caption='[[4qvd]], [[Resolution\|resolution]] 1.97Å' scene=''>	+	<StructureSection load='4qvd' size='340' side='right'caption='[[4qvd]], [[Resolution\|resolution]] 1.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qvd]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QVD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qvd]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QVD FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qvc\|4qvc]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qvc\|4qvc]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hfq ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=4qvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qvd OCA], [http://pdbe.org/4qvd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qvd RCSB], [http://www.ebi.ac.uk/pdbsum/4qvd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qvd 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=4qvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qvd OCA], [http://pdbe.org/4qvd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qvd RCSB], [http://www.ebi.ac.uk/pdbsum/4qvd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qvd ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Gong, Q G]]		[[Category: Gong, Q G]]
	[[Category: Li, F D]]		[[Category: Li, F D]]

OCA at 17:24, 9 March 2017

OCA — Thu, 09 Mar 2017 17:24:20 GMT

←Older revision		Revision as of 17:24, 9 March 2017
Line 1:		Line 1:
		+
	==E.coli Hfq in complex with RNA Ads==		==E.coli Hfq in complex with RNA Ads==
	<StructureSection load='4qvd' size='340' side='right' caption='[[4qvd]], [[Resolution\|resolution]] 1.97Å' scene=''>		<StructureSection load='4qvd' size='340' side='right' caption='[[4qvd]], [[Resolution\|resolution]] 1.97Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4qvd]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QVD FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qvd]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QVD FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qvc\|4qvc]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qvc\|4qvc]]</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=4qvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qvd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qvd RCSB], [http://www.ebi.ac.uk/pdbsum/4qvd PDBsum]</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=4qvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qvd OCA], [http://pdbe.org/4qvd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qvd RCSB], [http://www.ebi.ac.uk/pdbsum/4qvd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qvd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	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 4qvd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:49, 27 May 2015

OCA — Wed, 27 May 2015 15:49:34 GMT

←Older revision		Revision as of 15:49, 27 May 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==E.coli Hfq in complex with RNA Ads==
		+	<StructureSection load='4qvd' size='340' side='right' caption='[[4qvd]], [[Resolution\|resolution]] 1.97Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4qvd]] is a 7 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QVD FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qvc\|4qvc]]</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=4qvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qvd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qvd RCSB], [http://www.ebi.ac.uk/pdbsum/4qvd PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/C1IFD2_ECOLX C1IFD2_ECOLX]] 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. Also binds with high specificity to tRNAs.[HAMAP-Rule:MF_00436]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Small RNA OxyS is induced during oxidative stress in Escherichia coli and it is an Hfq-dependent negative regulator of mRNA translation. OxyS represses the translation of fhlA and rpoS mRNA, which encode the transcriptional activator and sigma(s) subunit of RNA polymerase, respectively. However, little is known regarding how Hfq, an RNA chaperone, interacts with OxyS at the atomic level. Here, using fluorescence polarization and tryptophan fluorescence quenching assays, we verified that the A-rich linker region of OxyS sRNA binds Hfq at its distal side. We also report two crystal structures of Hfq in complex with A-rich RNA fragments from this linker region. Both of these RNA fragments bind to the distal side of Hfq and adopt a different conformation compared with those previously reported for the (A-R-N)n tripartite recognition motif. Furthermore, using fluorescence polarization, electrophoresis mobility shift assays and in vivo translation assays, we found that an Hfq mutant, N48A, increases the binding affinity of OxyS for Hfq in vitro but is defective in the negative regulation of fhlA translation in vivo, suggesting that the normal function of OxyS depends on the details of the interaction with Hfq that may be related to the rapid recycling of Hfq in the cell.

-	~~The entry 4qvd is ON HOLD until Paper Publication~~	+	Structural insights into the recognition of the internal A-rich linker from OxyS sRNA by Escherichia coli Hfq.,Wang L, Wang W, Li F, Zhang J, Wu J, Gong Q, Shi Y Nucleic Acids Res. 2015 Feb 27;43(4):2400-11. doi: 10.1093/nar/gkv072. Epub 2015 , Feb 10. PMID:25670676<ref>PMID:25670676</ref>

-	~~Authors: Wang~~, L.J.~~, Wang, W~~.~~W., Li, F.D., Wu, J.H.,~~ Gong, Q.G~~., Shi, Y.Y.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~E.coli Hfq in complex with RNA Ads~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
-	[[Category: ~~Gong~~, ~~Q.G~~]]	+	__TOC__
-	[[Category: Wang, W.W]]	+	</StructureSection>
-	[[Category: Wu, J.H]]	+	[[Category: Gong, Q G]]
-	[[Category: ~~Shi, Y.Y~~]]	+	[[Category: Li, F D]]
-	[[Category: ~~Wang, L.J~~]]	+	[[Category: Shi, Y Y]]
-	[[Category: ~~Li, F.D~~]]	+	[[Category: Wang, L J]]
		+	[[Category: Wang, W W]]
		+	[[Category: Wu, J H]]
		+	[[Category: Rna]]
		+	[[Category: Rna binding protein-rna complex]]
		+	[[Category: Rna chaperone]]
		+	[[Category: Sm fold]]

OCA at 16:09, 24 December 2014

OCA — Wed, 24 Dec 2014 16:09:16 GMT

←Older revision		Revision as of 16:09, 24 December 2014
Line 6:		Line 6:

	Description: E.coli Hfq in complex with RNA Ads		Description: E.coli Hfq in complex with RNA Ads
		+	[[Category: Unreleased Structures]]
		+	[[Category: Gong, Q.G]]
		+	[[Category: Wang, W.W]]
		+	[[Category: Wu, J.H]]
		+	[[Category: Shi, Y.Y]]
		+	[[Category: Wang, L.J]]
		+	[[Category: Li, F.D]]

OCA at 09:25, 24 December 2014

OCA — Wed, 24 Dec 2014 09:25:25 GMT

←Older revision		Revision as of 09:25, 24 December 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Wang, L.J., Wang, W.W., Li, F.D., Wu, J.H., Gong, Q.G., Shi, Y.Y.		Authors: Wang, L.J., Wang, W.W., Li, F.D., Wu, J.H., Gong, Q.G., Shi, Y.Y.

	Description: E.coli Hfq in complex with RNA Ads		Description: E.coli Hfq in complex with RNA Ads

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

OCA — Wed, 23 Jul 2014 07:14:30 GMT

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

←Older revision

Revision as of 07:14, 23 July 2014

OCA: New page: '''Unreleased structure''' The entry 4qvd is ON HOLD Authors: Wang, L.J., Wang, W.W., Li, F.D., Wu, J.H., Gong, Q.G., Shi, Y.Y. Description: E.coli Hfq in complex with RNA Ads

OCA — Wed, 23 Jul 2014 07:14:28 GMT

New page: '''Unreleased structure''' The entry 4qvd is ON HOLD Authors: Wang, L.J., Wang, W.W., Li, F.D., Wu, J.H., Gong, Q.G., Shi, Y.Y. Description: E.coli Hfq in complex with RNA Ads

New page

'''Unreleased structure'''

The entry 4qvd is ON HOLD

Authors: Wang, L.J., Wang, W.W., Li, F.D., Wu, J.H., Gong, Q.G., Shi, Y.Y.

Description: E.coli Hfq in complex with RNA Ads