5l6m - Revision history

OCA at 16:08, 4 October 2023

2023-10-04T16:08:49Z

←Older revision		Revision as of 16:08, 4 October 2023
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	<StructureSection load='5l6m' size='340' side='right'caption='[[5l6m]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5l6m' size='340' side='right'caption='[[5l6m]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l6m]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cauvc Cauvc~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L6M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5L6M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l6m]] is a 12 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=5L6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5L6M FirstGlance]. <br>
-	</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=MLI:MALONATE+ION'>MLI</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]] 1.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5k8j\|5k8j]], [[5l6l\|5l6l]]</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=MLI:MALONATE+ION'>MLI</scene></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 CAUVC]), vapC, CC_0031 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190650 CAUVC])~~</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=5l6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l6m OCA], [https://pdbe.org/5l6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5l6m RCSB], [https://www.ebi.ac.uk/pdbsum/5l6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5l6m ProSAT]</span></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=5l6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l6m OCA], [~~http~~://pdbe.org/5l6m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5l6m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5l6m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5l6m 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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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cauvc~~]]	+	[[Category: Caulobacter vibrioides CB15]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bendtsen~~, K L~~]]	+	[[Category: Bendtsen KL]]
-	[[Category: Brodersen~~, D E~~]]	+	[[Category: Brodersen DE]]
-	[[Category: Luckmann, M]]	+	[[Category: Luckmann M]]
-	[[Category: Xu, K]]	+	[[Category: Xu K]]
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pin domain]]~~	+
-	~~[[Category: Ribonuclease]]~~	+
-	~~[[Category: Toxin-antitoxin~~]]	+

OCA at 06:58, 5 August 2020

2020-08-05T06:58:13Z

←Older revision		Revision as of 06:58, 5 August 2020
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	==Structure of Caulobacter crescentus VapBC1 (VapB1deltaC:VapC1 form)==		==Structure of Caulobacter crescentus VapBC1 (VapB1deltaC:VapC1 form)==
-	<StructureSection load='5l6m' size='340' side='right' caption='[[5l6m]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5l6m' size='340' side='right'caption='[[5l6m]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l6m]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L6M OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5L6M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l6m]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Cauvc Cauvc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L6M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5L6M 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>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>	+	</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=MLI:MALONATE+ION'>MLI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k8j\|5k8j]], [[5l6l\|5l6l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k8j\|5k8j]], [[5l6l\|5l6l]]</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=5l6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l6m OCA], [http://pdbe.org/5l6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l6m RCSB], [http://www.ebi.ac.uk/pdbsum/5l6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l6m 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 CAUVC]), vapC, CC_0031 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190650 CAUVC])</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=5l6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l6m OCA], [http://pdbe.org/5l6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l6m RCSB], [http://www.ebi.ac.uk/pdbsum/5l6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l6m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5l6m" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5l6m" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cauvc]]
		+	[[Category: Large Structures]]
	[[Category: Bendtsen, K L]]		[[Category: Bendtsen, K L]]
	[[Category: Brodersen, D E]]		[[Category: Brodersen, D E]]

OCA at 07:29, 18 January 2017

2017-01-18T07:29:06Z

←Older revision		Revision as of 07:29, 18 January 2017
Line 10:		Line 10:
	== 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 5l6m" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:25, 2 January 2017

2017-01-02T16:25:49Z

←Older revision		Revision as of 16:25, 2 January 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5l6m is ~~ON HOLD until Paper Publication~~	+	==Structure of Caulobacter crescentus VapBC1 (VapB1deltaC:VapC1 form)==
-		+	<StructureSection load='5l6m' size='340' side='right' caption='[[5l6m]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5l6m]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5L6M 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>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k8j\|5k8j]], [[5l6l\|5l6l]]</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=5l6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l6m OCA], [http://pdbe.org/5l6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l6m RCSB], [http://www.ebi.ac.uk/pdbsum/5l6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l6m 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 "5l6m" [edit=sysop:move=sysop]

2016-06-20T13:56:47Z

Protected "5l6m" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:56, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5l6m is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2016-06-20T13:56:46Z

New page: '''Unreleased structure''' The entry 5l6m is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5l6m is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]