4i8o - Revision history

OCA at 08:48, 9 November 2022

OCA — Wed, 09 Nov 2022 08:48:49 GMT

←Older revision		Revision as of 08:48, 9 November 2022
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	==Crystal structure of the toxin RnlA from Escherichia coli==		==Crystal structure of the toxin RnlA from Escherichia coli==
-	<StructureSection load='4i8o' size='340' side='right' caption='[[4i8o]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='4i8o' size='340' side='right'caption='[[4i8o]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4i8o]] is a 2 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=4I8O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4I8O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4i8o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4I8O FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yfjN, b2630, JW2611 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])~~</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=4i8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8o OCA], [https://pdbe.org/4i8o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4i8o RCSB], [https://www.ebi.ac.uk/pdbsum/4i8o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4i8o 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=4i8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8o OCA], [~~http~~://pdbe.org/4i8o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4i8o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4i8o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4i8o ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RNLA_ECOLI RNLA_ECOLI]] Toxic component of a toxin-antitoxin (TA) module. A stable (half-life 27.6 minutes) endoribonuclease that in the absence of cognate antitoxin RnlB causes generalized RNA degradation. Degrades late enterobacteria phage T4 mRNAs, protecting the host against T4 reproduction. Activity is inhibited by cognate antitoxin RnlB and by enterobacteria phage T4 protein Dmd. Targets cyaA mRNA.<ref>PMID:17895580</ref> <ref>PMID:19019153</ref> <ref>PMID:20980243</ref> <ref>PMID:22403819</ref>	+	[https://www.uniprot.org/uniprot/RNLA_ECOLI RNLA_ECOLI] Toxic component of a toxin-antitoxin (TA) module. A stable (half-life 27.6 minutes) endoribonuclease that in the absence of cognate antitoxin RnlB causes generalized RNA degradation. Degrades late enterobacteria phage T4 mRNAs, protecting the host against T4 reproduction. Activity is inhibited by cognate antitoxin RnlB and by enterobacteria phage T4 protein Dmd. Targets cyaA mRNA.<ref>PMID:17895580</ref> <ref>PMID:19019153</ref> <ref>PMID:20980243</ref> <ref>PMID:22403819</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: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
-	[[Category: ~~Dong, Y H~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Gao, Z Q~~]]	+	[[Category: Dong YH]]
-	[[Category: ~~Wei, Y~~]]	+	[[Category: Gao ZQ]]
-	[[Category: ~~Zhang, H~~]]	+	[[Category: Wei Y]]
-	[[Category: ~~Toxin]]~~	+	[[Category: Zhang H]]
-	~~[[Category: Toxin protein~~]]	+

OCA at 20:56, 5 August 2016

OCA — Fri, 05 Aug 2016 20:56:39 GMT

←Older revision		Revision as of 20:56, 5 August 2016
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		+
	==Crystal structure of the toxin RnlA from Escherichia coli==		==Crystal structure of the toxin RnlA from Escherichia coli==
	<StructureSection load='4i8o' size='340' side='right' caption='[[4i8o]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4i8o' size='340' side='right' caption='[[4i8o]], [[Resolution\|resolution]] 2.10Å' scene=''>
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	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yfjN, b2630, JW2611 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yfjN, b2630, JW2611 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4i8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i8o RCSB], [http://www.ebi.ac.uk/pdbsum/4i8o 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=4i8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8o OCA], [http://pdbe.org/4i8o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i8o RCSB], [http://www.ebi.ac.uk/pdbsum/4i8o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i8o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 4i8o" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:50, 25 December 2014

OCA — Thu, 25 Dec 2014 21:50:56 GMT

←Older revision		Revision as of 21:50, 25 December 2014
Line 7:		Line 7:
	<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=4i8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i8o RCSB], [http://www.ebi.ac.uk/pdbsum/4i8o 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=4i8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i8o RCSB], [http://www.ebi.ac.uk/pdbsum/4i8o PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNLA_ECOLI RNLA_ECOLI]] Toxic component of a toxin-antitoxin (TA) module. A stable (half-life 27.6 minutes) endoribonuclease that in the absence of cognate antitoxin RnlB causes generalized RNA degradation. Degrades late enterobacteria phage T4 mRNAs, protecting the host against T4 reproduction. Activity is inhibited by cognate antitoxin RnlB and by enterobacteria phage T4 protein Dmd. Targets cyaA mRNA.<ref>PMID:17895580</ref> <ref>PMID:19019153</ref> <ref>PMID:20980243</ref> <ref>PMID:22403819</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:24, 3 December 2014

OCA — Wed, 03 Dec 2014 07:24:11 GMT

←Older revision		Revision as of 07:24, 3 December 2014
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-	~~{{STRUCTURE_4i8o\| PDB=4i8o \| SCENE= }}~~	+	==Crystal structure of the toxin RnlA from Escherichia coli==
-	===Crystal structure of the toxin RnlA from Escherichia coli===	+	<StructureSection load='4i8o' size='340' side='right' caption='[[4i8o]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24112600}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4i8o]] is a 2 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=4I8O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I8O FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yfjN, b2630, JW2611 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4i8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i8o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i8o RCSB], [http://www.ebi.ac.uk/pdbsum/4i8o PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Escherichia coli RnlA-RnlB is a newly identified toxin-antitoxin (TA) system that plays a role in bacteriophage resistance. RnlA functions as a toxin with mRNA endoribonuclease activity and the cognate antitoxin RnlB inhibits RnlA toxicity in E. coli cells. Interestingly, T4 phage encodes the antitoxin Dmd, which acts against RnlA to promote its own propagation, suggesting that RnlA-Dmd represents a novel TA system. Here, we have determined the crystal structure of RnlA refined to 2.10 A. RnlA is composed of three independent domains: NTD (N-terminal domain), NRD (N repeated domain) and DBD (Dmd binding domain), which is an organization not previously observed among known toxin structures. Small-angle X-ray scattering (SAXS) analysis revealed that RnlA forms a dimer in solution via interactions between the DBDs from both monomers. The in vitro and in vivo functional studies showed that among the three domains, only the DBD is responsible for recognition and inhibition by Dmd and subcellular location of RnlA. In particular, the helix located at the C-terminus of DBD plays a vital role in binding Dmd. Our comprehensive studies reveal the key region responsible for RnlA toxicity and provide novel insights into its structure-function relationship.

-	~~==Function==~~	+	Structure-function studies of Escherichia coli RnlA reveal a novel toxin structure involved in bacteriophage resistance.,Wei Y, Gao ZQ, Otsuka Y, Naka K, Yonesaki T, Zhang H, Dong YH Mol Microbiol. 2013 Sep 30. doi: 10.1111/mmi.12409. PMID:24112600<ref>PMID:24112600</ref>
-	~~[[http://www.uniprot.org/uniprot/RNLA_ECOLI RNLA_ECOLI]] Toxic component~~ of a toxin~~-antitoxin (TA) module. A stable (half-life 27.6 minutes) endoribonuclease that~~ in ~~the absence of cognate antitoxin RnlB causes generalized RNA degradation~~. ~~Degrades late enterobacteria phage T4 mRNAs~~, ~~protecting the host against T4 reproduction~~. ~~Activity is inhibited by cognate antitoxin RnlB and by enterobacteria phage T4 protein Dmd~~. ~~Targets cyaA mRNA~~.~~<ref>PMID:17895580<~~/~~ref> <ref>~~PMID:~~19019153</ref> <ref>PMID:20980243</ref>~~ <ref>PMID:~~22403819~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4i8o]] is~~ a ~~2 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=4I8O OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:024112600</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
-	[[Category: Dong, Y H.]]	+	[[Category: Dong, Y H]]
-	[[Category: Gao, Z Q.]]	+	[[Category: Gao, Z Q]]
	[[Category: Wei, Y]]		[[Category: Wei, Y]]
	[[Category: Zhang, H]]		[[Category: Zhang, H]]
	[[Category: Toxin]]		[[Category: Toxin]]
	[[Category: Toxin protein]]		[[Category: Toxin protein]]

OCA at 12:11, 11 December 2013

OCA — Wed, 11 Dec 2013 12:11:16 GMT

←Older revision		Revision as of 12:11, 11 December 2013
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	==About this Structure==		==About this Structure==
-	[[4i8o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8O OCA].	+	[[4i8o]] is a 2 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=4I8O OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:024112600</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:024112600</ref><references group="xtra"/><references/>
-	[[Category: ~~Escherichia coli k-12~~]]	+	[[Category: Ecoli]]
	[[Category: Dong, Y H.]]		[[Category: Dong, Y H.]]
	[[Category: Gao, Z Q.]]		[[Category: Gao, Z Q.]]

OCA at 06:40, 23 October 2013

OCA — Wed, 23 Oct 2013 06:40:02 GMT

←Older revision		Revision as of 06:40, 23 October 2013
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-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4i8o\| PDB=4i8o \| SCENE= }}
		+	===Crystal structure of the toxin RnlA from Escherichia coli===
		+	{{ABSTRACT_PUBMED_24112600}}

-	~~The entry 4i8o~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/RNLA_ECOLI RNLA_ECOLI]] Toxic component of a toxin-antitoxin (TA) module. A stable (half-life 27.6 minutes) endoribonuclease that in the absence of cognate antitoxin RnlB causes generalized RNA degradation. Degrades late enterobacteria phage T4 mRNAs, protecting the host against T4 reproduction. Activity is inhibited by cognate antitoxin RnlB and by enterobacteria phage T4 protein Dmd. Targets cyaA mRNA.<ref>PMID:17895580</ref> <ref>PMID:19019153</ref> <ref>PMID:20980243</ref> <ref>PMID:22403819</ref>

-	~~Authors~~: ~~Wei, Y, Gao, Z~~.Q.~~, Zhang, H, Dong, Y~~.H.	+	==About this Structure==
		+	[[4i8o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I8O OCA].

-	~~Description~~: ~~Crystal structure of the toxin RnlA from~~ Escherichia coli	+	==Reference==
		+	<ref group="xtra">PMID:024112600</ref><references group="xtra"/><references/>
		+	[[Category: Escherichia coli k-12]]
		+	[[Category: Dong, Y H.]]
		+	[[Category: Gao, Z Q.]]
		+	[[Category: Wei, Y]]
		+	[[Category: Zhang, H]]
		+	[[Category: Toxin]]
		+	[[Category: Toxin protein]]

OCA at 08:53, 2 January 2013

OCA — Wed, 02 Jan 2013 08:53:58 GMT

←Older revision		Revision as of 08:53, 2 January 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4i8o is ON HOLD	+	The entry 4i8o is ON HOLD until Paper Publication

	Authors: Wei, Y, Gao, Z.Q., Zhang, H, Dong, Y.H.		Authors: Wei, Y, Gao, Z.Q., Zhang, H, Dong, Y.H.

	Description: Crystal structure of the toxin RnlA from Escherichia coli		Description: Crystal structure of the toxin RnlA from Escherichia coli

OCA: Protected "4i8o" [edit=sysop:move=sysop]

OCA — Wed, 12 Dec 2012 20:50:47 GMT

Protected "4i8o" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:50, 12 December 2012

OCA: New page: '''Unreleased structure''' The entry 4i8o is ON HOLD Authors: Wei, Y, Gao, Z.Q., Zhang, H, Dong, Y.H. Description: Crystal structure of the toxin RnlA from Escherichia coli

OCA — Wed, 12 Dec 2012 20:50:46 GMT

New page: '''Unreleased structure''' The entry 4i8o is ON HOLD Authors: Wei, Y, Gao, Z.Q., Zhang, H, Dong, Y.H. Description: Crystal structure of the toxin RnlA from Escherichia coli

New page

'''Unreleased structure'''

The entry 4i8o is ON HOLD

Authors: Wei, Y, Gao, Z.Q., Zhang, H, Dong, Y.H.

Description: Crystal structure of the toxin RnlA from Escherichia coli