7els - Revision history

OCA at 16:56, 29 November 2023

OCA — Wed, 29 Nov 2023 16:56:12 GMT

←Older revision		Revision as of 16:56, 29 November 2023
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	<StructureSection load='7els' size='340' side='right'caption='[[7els]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='7els' size='340' side='right'caption='[[7els]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7els]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ELS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ELS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7els]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ideonella_sp._B508-1 Ideonella sp. B508-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ELS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ELS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=7els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7els OCA], [https://pdbe.org/7els PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7els RCSB], [https://www.ebi.ac.uk/pdbsum/7els PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7els 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=7els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7els OCA], [https://pdbe.org/7els PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7els RCSB], [https://www.ebi.ac.uk/pdbsum/7els PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7els ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7els" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7els" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ideonella sp. B508-1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ren~~, A M~~]]	+	[[Category: Ren AM]]
-	[[Category: Xu~~, X C]]~~	+	[[Category: Xu XC]]
-	~~[[Category: 8-azaxanthine]]~~	+
-	~~[[Category: Riboswitch]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 09:14, 21 July 2021

OCA — Wed, 21 Jul 2021 09:14:38 GMT

←Older revision		Revision as of 09:14, 21 July 2021
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	==Crystal structure of xanthine riboswitch with 8-azaxanthine==		==Crystal structure of xanthine riboswitch with 8-azaxanthine==
-	<StructureSection load='7els' size='340' side='right'caption='[[7els]]' scene=''>	+	<StructureSection load='7els' size='340' side='right'caption='[[7els]], [[Resolution\|resolution]] 3.00Å' 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=7ELS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ELS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7els]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ELS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ELS FirstGlance]. <br>
-	</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=7els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7els OCA], [https://pdbe.org/7els PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7els RCSB], [https://www.ebi.ac.uk/pdbsum/7els PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7els 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=AZA:8-AZAXANTHINE'>AZA</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=7els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7els OCA], [https://pdbe.org/7els PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7els RCSB], [https://www.ebi.ac.uk/pdbsum/7els PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7els ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson-Crick base pair to junction J2. Xanthine inserts between a G-U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.
		+
		+	Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition.,Xu X, Egger M, Chen H, Bartosik K, Micura R, Ren A Nucleic Acids Res. 2021 Jun 14. pii: 6298625. doi: 10.1093/nar/gkab486. PMID:34125892<ref>PMID:34125892</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7els" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ren AM]]	+	[[Category: Ren, A M]]
-	[[Category: Xu XC]]	+	[[Category: Xu, X C]]
		+	[[Category: 8-azaxanthine]]
		+	[[Category: Riboswitch]]
		+	[[Category: Rna]]

OCA at 03:33, 2 July 2021

OCA — Fri, 02 Jul 2021 03:33:29 GMT

←Older revision		Revision as of 03:33, 2 July 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7els ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of xanthine riboswitch with 8-azaxanthine==
-		+	<StructureSection load='7els' size='340' side='right'caption='[[7els]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ELS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ELS FirstGlance]. <br>
-	~~Description~~:	+	</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=7els FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7els OCA], [https://pdbe.org/7els PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7els RCSB], [https://www.ebi.ac.uk/pdbsum/7els PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7els ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Ren AM]]
		+	[[Category: Xu XC]]

OCA at 08:02, 12 May 2021

OCA — Wed, 12 May 2021 08:02:39 GMT

←Older revision		Revision as of 08:02, 12 May 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7els is ON HOLD	+	The entry 7els is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7els" [edit=sysop:move=sysop]

OCA — Wed, 21 Apr 2021 06:04:52 GMT

Protected "7els" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:04, 21 April 2021

OCA: New page: '''Unreleased structure''' The entry 7els is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 21 Apr 2021 06:04:50 GMT

New page: '''Unreleased structure''' The entry 7els is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7els is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]