6n2v - Revision history

OCA at 06:44, 11 October 2023

OCA — Wed, 11 Oct 2023 06:44:04 GMT

←Older revision		Revision as of 06:44, 11 October 2023
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	<StructureSection load='6n2v' size='340' side='right'caption='[[6n2v]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='6n2v' size='340' side='right'caption='[[6n2v]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n2v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca.weizmann~~.~~ac.il/oca-docs~~/fgij/fg.htm?mol=6N2V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n2v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_oryzae Xanthomonas oryzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N2V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR~~</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]] 2.85Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP~~</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></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=6n2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2v OCA], [~~http~~://pdbe.org/6n2v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n2v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n2v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2v ProSAT]</span></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=6n2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2v OCA], [https://pdbe.org/6n2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n2v RCSB], [https://www.ebi.ac.uk/pdbsum/6n2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2v ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 6n2v" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6n2v" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ke, A~~]]	+	[[Category: Xanthomonas oryzae]]
-	[[Category: ~~Price, I R~~]]	+	[[Category: Ke A]]
-	[[Category: ~~Manganese]]~~	+	[[Category: Price IR]]
-	~~[[Category: Riboswitch]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 10:27, 2 October 2019

OCA — Wed, 02 Oct 2019 10:27:30 GMT

←Older revision		Revision as of 10:27, 2 October 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6n2v is ~~ON HOLD until Paper~~ Publication	+	==Manganese riboswitch from Xanthmonas oryzae bound to Mn(II)==
		+	<StructureSection load='6n2v' size='340' side='right'caption='[[6n2v]], [[Resolution\|resolution]] 2.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6n2v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N2V FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></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=6n2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2v OCA], [http://pdbe.org/6n2v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n2v RCSB], [http://www.ebi.ac.uk/pdbsum/6n2v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2v ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The widespread Mn(2+)-sensing yybP-ykoY riboswitch controls the expression of bacterial Mn(2+) homeostasis genes. Here, we first determine the crystal structure of the ligand-bound yybP-ykoY riboswitch aptamer from Xanthomonas oryzae at 2.96 A resolution, revealing two conformations with docked four-way junction (4WJ) and incompletely coordinated metal ions. In >100 micros of MD simulations, we observe that loss of divalents from the core triggers local structural perturbations in the adjacent docking interface, laying the foundation for signal transduction to the regulatory switch helix. Using single-molecule FRET, we unveil a previously unobserved extended 4WJ conformation that samples transient docked states in the presence of Mg(2+). Only upon adding sub-millimolar Mn(2+), however, can the 4WJ dock stably, a feature lost upon mutation of an adenosine contacting Mn(2+) in the core. These observations illuminate how subtly differing ligand preferences of competing metal ions become amplified by the coupling of local with global RNA dynamics.

-	~~Authors:~~ Price, ~~I.R.~~, Ke, A.	+	Local-to-global signal transduction at the core of a Mn(2+) sensing riboswitch.,Suddala KC, Price IR, Dandpat SS, Janecek M, Kuhrova P, Sponer J, Banas P, Ke A, Walter NG Nat Commun. 2019 Sep 20;10(1):4304. doi: 10.1038/s41467-019-12230-5. PMID:31541094<ref>PMID:31541094</ref>

-	~~Description~~: ~~Manganese riboswitch from Xanthmonas oryzae bound to Mn(II)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6n2v" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ke, A]]		[[Category: Ke, A]]
-	[[Category: Price, I.R]]	+	[[Category: Price, I R]]
		+	[[Category: Manganese]]
		+	[[Category: Riboswitch]]
		+	[[Category: Rna]]

OCA at 06:24, 30 January 2019

OCA — Wed, 30 Jan 2019 06:24:55 GMT

←Older revision		Revision as of 06:24, 30 January 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n2v is ON HOLD	+	The entry 6n2v is ON HOLD until Paper Publication

	Authors: Price, I.R., Ke, A.		Authors: Price, I.R., Ke, A.

OCA: Protected "6n2v" [edit=sysop:move=sysop]

OCA — Sun, 02 Dec 2018 19:10:55 GMT

Protected "6n2v" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:10, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n2v is ON HOLD Authors: Price, I.R., Ke, A. Description: Manganese riboswitch from Xanthmonas oryzae bound to Mn(II) [[Category: Unreleased Struct...

OCA — Sun, 02 Dec 2018 19:10:54 GMT

New page: '''Unreleased structure''' The entry 6n2v is ON HOLD Authors: Price, I.R., Ke, A. Description: Manganese riboswitch from Xanthmonas oryzae bound to Mn(II) [[Category: Unreleased Struct...

New page

'''Unreleased structure'''

The entry 6n2v is ON HOLD

Authors: Price, I.R., Ke, A.

Description: Manganese riboswitch from Xanthmonas oryzae bound to Mn(II)
[[Category: Unreleased Structures]]
[[Category: Ke, A]]
[[Category: Price, I.R]]