6t46 - Revision history

OCA at 12:54, 24 January 2024

OCA — Wed, 24 Jan 2024 12:54:29 GMT

←Older revision		Revision as of 12:54, 24 January 2024
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	<StructureSection load='6t46' size='340' side='right'caption='[[6t46]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='6t46' size='340' side='right'caption='[[6t46]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6t46]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacna Bacna~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T46 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6T46 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6t46]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._natto Bacillus subtilis subsp. natto]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6T46 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.45Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6t3h\|6t3h]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">rapA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86029 BACNA])~~</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=6t46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t46 OCA], [https://pdbe.org/6t46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6t46 RCSB], [https://www.ebi.ac.uk/pdbsum/6t46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6t46 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=6t46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t46 OCA], [~~http~~://pdbe.org/6t46 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6t46 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6t46 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6t46 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E9RIY6_BACNA E9RIY6_BACNA]
	<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 6t46" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6t46" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Response regulator 3D structure\|Response regulator 3D structure]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacna~~]]	+	[[Category: Bacillus subtilis subsp. natto]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bernardo, N]]	+	[[Category: Bernardo N]]
-	[[Category: Boer~~, D R~~]]	+	[[Category: Boer DR]]
-	[[Category: Crespo, I]]	+	[[Category: Crespo I]]
-	[[Category: Meijer~~, W J.J]]~~	+	[[Category: Meijer WJJ]]
-	~~[[Category: Conjugation]]~~	+
-	~~[[Category: Response regulator]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 11:31, 22 July 2020

OCA — Wed, 22 Jul 2020 11:31:40 GMT

←Older revision		Revision as of 11:31, 22 July 2020
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	==Structure of the Rap conjugation gene regulator of the plasmid pLS20 in complex with the Phr* peptide==		==Structure of the Rap conjugation gene regulator of the plasmid pLS20 in complex with the Phr* peptide==
-	<StructureSection load='6t46' size='340' side='right'caption='[[6t46]]' scene=''>	+	<StructureSection load='6t46' size='340' side='right'caption='[[6t46]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T46 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6T46 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6t46]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacna Bacna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T46 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6T46 FirstGlance]. <br>
-	</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=6t46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t46 OCA], [http://pdbe.org/6t46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t46 RCSB], [http://www.ebi.ac.uk/pdbsum/6t46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t46 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6t3h\|6t3h]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rapA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=86029 BACNA])</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=6t46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t46 OCA], [http://pdbe.org/6t46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t46 RCSB], [http://www.ebi.ac.uk/pdbsum/6t46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t46 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Quorum sensing allows bacterial cells to communicate through the release of soluble signaling molecules into the surrounding medium. It plays a pivotal role in controlling bacterial conjugation in Gram-positive cells, a process that has tremendous impact on health. Intracellular regulatory proteins of the RRNPP family are common targets of these signaling molecules. The RRNPP family of gene regulators bind signaling molecules at their C-terminal domain (CTD), but have highly divergent functionalities at their N-terminal effector domains (NTD). This divergence is also reflected in the functional states of the proteins, and is highly interesting from an evolutionary perspective. RappLS20 is an RRNPP encoded on the Bacillus subtilis plasmid pLS20. It relieves the gene repression effectuated by RcopLS20 in the absence of the mature pLS20 signaling peptide PhrpLS20. We report here an in-depth structural study of apo and PhrpLS20-bound states of RappLS20 at various levels of atomic detail. We show that apo-RappLS20 is dimeric and that PhrpLS20-bound Rap forms NTD-mediated tetramers. In addition, we show that RappLS20 binds RcopLS20 directly in the absence of PhrpLS20 and that addition of Phr*pLS20 releases RcopLS20 from RappLS20. This allows RcopLS20 to bind the promotor region of crucial conjugation genes blocking their expression.
		+
		+	Inactivation of the dimeric RappLS20 anti-repressor of the conjugation operon is mediated by peptide-induced tetramerization.,Crespo I, Bernardo N, Miguel-Arribas A, Singh PK, Luque-Ortega JR, Alfonso C, Malfois M, Meijer WJJ, Boer DR Nucleic Acids Res. 2020 Jul 13. pii: 5870671. doi: 10.1093/nar/gkaa540. PMID:32658272<ref>PMID:32658272</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6t46" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacna]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bernardo N]]	+	[[Category: Bernardo, N]]
-	[[Category: Boer DR]]	+	[[Category: Boer, D R]]
-	[[Category: Crespo I]]	+	[[Category: Crespo, I]]
-	[[Category: Meijer ~~WJJ~~]]	+	[[Category: Meijer, W J.J]]
		+	[[Category: Conjugation]]
		+	[[Category: Response regulator]]
		+	[[Category: Transcription]]

OCA at 06:23, 25 June 2020

OCA — Thu, 25 Jun 2020 06:23:06 GMT

←Older revision		Revision as of 06:23, 25 June 2020
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-	'''Unreleased structure'''

-	~~The entry 6t46 is ON HOLD~~	+	==Structure of the Rap conjugation gene regulator of the plasmid pLS20 in complex with the Phr* peptide==
-		+	<StructureSection load='6t46' size='340' side='right'caption='[[6t46]]' scene=''>
-	~~Authors: Crespo, I., Bernardo, N., Meijer, W.J.J., Boer, D.R.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6T46 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6T46 FirstGlance]. <br>
-	~~Description:~~ Structure of the Rap conjugation gene regulator of the plasmid pLS20 in complex with the Phr* peptide	+	</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=6t46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6t46 OCA], [http://pdbe.org/6t46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6t46 RCSB], [http://www.ebi.ac.uk/pdbsum/6t46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6t46 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Bernardo, N]]	+	__TOC__
-	[[Category: Boer~~, D.R~~]]	+	</StructureSection>
-	[[Category: Crespo, I]]	+	[[Category: Large Structures]]
-	[[Category: Meijer~~, W.J.J~~]]	+	[[Category: Bernardo N]]
		+	[[Category: Boer DR]]
		+	[[Category: Crespo I]]
		+	[[Category: Meijer WJJ]]

OCA: Protected "6t46" [edit=sysop:move=sysop]

OCA — Wed, 23 Oct 2019 04:59:21 GMT

Protected "6t46" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:59, 23 October 2019

OCA: New page: '''Unreleased structure''' The entry 6t46 is ON HOLD Authors: Crespo, I., Bernardo, N., Meijer, W.J.J., Boer, D.R. Description: Structure of the Rap conjugation gene regulator of the p...

OCA — Wed, 23 Oct 2019 04:59:19 GMT

New page: '''Unreleased structure''' The entry 6t46 is ON HOLD Authors: Crespo, I., Bernardo, N., Meijer, W.J.J., Boer, D.R. Description: Structure of the Rap conjugation gene regulator of the p...

New page

'''Unreleased structure'''

The entry 6t46 is ON HOLD

Authors: Crespo, I., Bernardo, N., Meijer, W.J.J., Boer, D.R.

Description: Structure of the Rap conjugation gene regulator of the plasmid pLS20 in complex with the Phr* peptide
[[Category: Unreleased Structures]]
[[Category: Bernardo, N]]
[[Category: Boer, D.R]]
[[Category: Crespo, I]]
[[Category: Meijer, W.J.J]]