5k8j - Revision history

OCA at 10:43, 27 September 2023

OCA — Wed, 27 Sep 2023 10:43:08 GMT

←Older revision		Revision as of 10:43, 27 September 2023
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	==Structure of Caulobacter crescentus VapBC1 (apo form)==		==Structure of Caulobacter crescentus VapBC1 (apo form)==
-	<StructureSection load='5k8j' size='340' side='right' caption='[[5k8j]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5k8j' size='340' side='right'caption='[[5k8j]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k8j]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Caucr Caucr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K8J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k8j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides_CB15 Caulobacter vibrioides CB15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K8J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~></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]] 1.6Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[5l6l\|5l6l]], [[5l6m\|5l6m]]</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=5k8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8j OCA], [https://pdbe.org/5k8j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k8j RCSB], [https://www.ebi.ac.uk/pdbsum/5k8j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8j ProSAT]</span></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b></td><td class="sblockDat">CC_0032 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190650 CAUCR]), vapC, CC_0031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190650 CAUCR])</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=5k8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8j OCA], [~~http~~://pdbe.org/5k8j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k8j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k8j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8j ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~Q9AC35_CAUCR Q9AC35_CAUCR]] Toxic component of a toxin-antitoxin (TA) module. An RNase.[HAMAP-Rule:MF_00265~~]	+	[https://www.uniprot.org/uniprot/Q9AC34_CAUVC Q9AC34_CAUVC]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5k8j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5k8j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Caucr~~]]	+	[[Category: Caulobacter vibrioides CB15]]
-	[[Category: ~~Bendtsen, K L~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Brodersen, D E~~]]	+	[[Category: Bendtsen KL]]
-	[[Category: ~~Luckmann, M~~]]	+	[[Category: Brodersen DE]]
-	[[Category: ~~Xu, K~~]]	+	[[Category: Luckmann M]]
-	[[Category: ~~Dna-binding]]~~	+	[[Category: Xu K]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pin domain]]~~	+
-	~~[[Category: Ribonuclease]]~~	+
-	~~[[Category: Toxin-antitoxin~~]]	+

OCA at 08:08, 17 January 2018

OCA — Wed, 17 Jan 2018 08:08:14 GMT

←Older revision		Revision as of 08:08, 17 January 2018
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	<StructureSection load='5k8j' size='340' side='right' caption='[[5k8j]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5k8j' size='340' side='right' caption='[[5k8j]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k8j]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k8j]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Caucr Caucr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5l6l\|5l6l]], [[5l6m\|5l6m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5l6l\|5l6l]], [[5l6m\|5l6m]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CC_0032 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190650 CAUCR]), vapC, CC_0031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190650 CAUCR])</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=5k8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8j OCA], [http://pdbe.org/5k8j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8j RCSB], [http://www.ebi.ac.uk/pdbsum/5k8j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8j 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=5k8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8j OCA], [http://pdbe.org/5k8j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8j RCSB], [http://www.ebi.ac.uk/pdbsum/5k8j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8j ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Caucr]]
	[[Category: Bendtsen, K L]]		[[Category: Bendtsen, K L]]
	[[Category: Brodersen, D E]]		[[Category: Brodersen, D E]]

OCA at 08:19, 18 January 2017

OCA — Wed, 18 Jan 2017 08:19:02 GMT

←Older revision		Revision as of 08:19, 18 January 2017
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/Q9AC35_CAUCR Q9AC35_CAUCR]] Toxic component of a toxin-antitoxin (TA) module. An RNase.[HAMAP-Rule:MF_00265]		[[http://www.uniprot.org/uniprot/Q9AC35_CAUCR Q9AC35_CAUCR]] Toxic component of a toxin-antitoxin (TA) module. An RNase.[HAMAP-Rule:MF_00265]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Expression of bacterial type II toxin-antitoxin (TA) systems is regulated at the transcriptional level through direct binding of the antitoxin to pseudo-palindromic sequences on operator DNA. In this context, the toxin functions as a co-repressor by stimulating DNA binding through direct interaction with the antitoxin. Here, we determine crystal structures of the complete 90 kDa heterooctameric VapBC1 complex from Caulobacter crescentus CB15 both in isolation and bound to its cognate DNA operator sequence at 1.6 and 2.7 A resolution, respectively. DNA binding is associated with a dramatic architectural rearrangement of conserved TA interactions in which C-terminal extended structures of the antitoxin VapB1 swap positions to interlock the complex in the DNA-bound state. We further show that a pseudo-palindromic protein sequence in the antitoxin is responsible for this interaction and required for binding and inactivation of the VapC1 toxin dimer. Sequence analysis of 4127 orthologous VapB sequences reveals that such palindromic protein sequences are widespread and unique to bacterial and archaeal VapB antitoxins suggesting a general principle governing regulation of VapBC TA systems. Finally, a structure of C-terminally truncated VapB1 bound to VapC1 reveals discrete states of the TA interaction that suggest a structural basis for toxin activation in vivo.
		+
		+	Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding.,Bendtsen KL, Xu K, Luckmann M, Winther KS, Shah SA, Pedersen CN, Brodersen DE Nucleic Acids Res. 2016 Dec 19. pii: gkw1266. doi: 10.1093/nar/gkw1266. PMID:27998932<ref>PMID:27998932</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5k8j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:24, 2 January 2017

OCA — Mon, 02 Jan 2017 16:24:56 GMT

←Older revision		Revision as of 16:24, 2 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k8j is ~~ON HOLD until Paper Publication~~	+	==Structure of Caulobacter crescentus VapBC1 (apo form)==
-		+	<StructureSection load='5k8j' size='340' side='right' caption='[[5k8j]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5k8j]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8J FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5l6l\|5l6l]], [[5l6m\|5l6m]]</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=5k8j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8j OCA], [http://pdbe.org/5k8j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8j RCSB], [http://www.ebi.ac.uk/pdbsum/5k8j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8j ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q9AC35_CAUCR Q9AC35_CAUCR]] Toxic component of a toxin-antitoxin (TA) module. An RNase.[HAMAP-Rule:MF_00265]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bendtsen, K L]]
		+	[[Category: Brodersen, D E]]
		+	[[Category: Luckmann, M]]
		+	[[Category: Xu, K]]
		+	[[Category: Dna-binding]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pin domain]]
		+	[[Category: Ribonuclease]]
		+	[[Category: Toxin-antitoxin]]

OCA: Protected "5k8j" [edit=sysop:move=sysop]

OCA — Mon, 20 Jun 2016 13:33:42 GMT

Protected "5k8j" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:33, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k8j is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Mon, 20 Jun 2016 13:33:41 GMT

New page: '''Unreleased structure''' The entry 5k8j is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5k8j is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]