6ez0 - Revision history

OCA at 10:44, 14 June 2023

2023-06-14T10:44:48Z

←Older revision		Revision as of 10:44, 14 June 2023
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	==Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding==		==Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding==
-	<StructureSection load='6ez0' size='340' side='right'caption='[[6ez0~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='6ez0' size='340' side='right'caption='[[6ez0]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ez0]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EZ0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6EZ0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ez0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EZ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EZ0 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=U37:URIDINE+5-MONOTHIOPHOSPHATE'>U37</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=U37:URIDINE+5-MONOTHIOPHOSPHATE'>U37</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2aht\|2aht]]~~</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=6ez0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ez0 OCA], [https://pdbe.org/6ez0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ez0 RCSB], [https://www.ebi.ac.uk/pdbsum/6ez0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ez0 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=6ez0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ez0 OCA], [~~http~~://pdbe.org/6ez0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ez0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ez0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ez0 ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	==See Also==		==See Also==
-	*[[Ribozyme\|Ribozyme]]	+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Besic, E]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Erat~~, M C~~]]	+	[[Category: Besic E]]
-	[[Category: Johannsen, S]]	+	[[Category: Erat MC]]
-	[[Category: Oberhuber, M]]	+	[[Category: Johannsen S]]
-	[[Category: Sigel~~, R K.O]]~~	+	[[Category: Oberhuber M]]
-	~~[[Category: Rna]]~~	+	[[Category: Sigel RKO]]
-	~~[[Category: Thiophosphate group ii intron branch-adenosine hairpin tetraloop~~]]	+

OCA at 13:25, 10 May 2019

2019-05-10T13:25:19Z

←Older revision		Revision as of 13:25, 10 May 2019
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	==Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding==		==Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding==
-	<StructureSection load='6ez0' size='340' side='right' caption='[[6ez0]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='6ez0' size='340' side='right'caption='[[6ez0]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ez0]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EZ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EZ0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ez0]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EZ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EZ0 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 6ez0" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ez0" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Besic, E]]		[[Category: Besic, E]]
	[[Category: Erat, M C]]		[[Category: Erat, M C]]

OCA at 05:53, 3 January 2018

2018-01-03T05:53:05Z

←Older revision		Revision as of 05:53, 3 January 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 6ez0 is ~~ON HOLD~~	+	==Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding==
		+	<StructureSection load='6ez0' size='340' side='right' caption='[[6ez0]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ez0]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EZ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EZ0 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=U37:URIDINE+5-MONOTHIOPHOSPHATE'>U37</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2aht\|2aht]]</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=6ez0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ez0 OCA], [http://pdbe.org/6ez0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ez0 RCSB], [http://www.ebi.ac.uk/pdbsum/6ez0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ez0 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Group II introns are large self-splicing ribozymes that require high amounts of monovalent and divalent metal ions for folding and catalysis under in vitro conditions. Domain 6 of these ribozymes contains a highly conserved adenosine whose 2'-OH acts as a nucleophile during self-cleavage via the branching pathway. We have previously suggested a divalent metal ion that binds to the major groove at the GU wobble pair above the branch-A in a minimal, but active branch domain construct (D6-27) from the yeast mitochondrial intron Sc.ai5gamma. Here we characterize metal ion binding to the phosphate oxygens at the branch site. In vitro transcription yielded a D6-27 construct where all R P oxygens of the uridine phosphate groups are replaced by sulfur (alpha-thio-D6-27). We determined its NMR structure, the second RNA-only structure containing thiophosphate groups. [(31)P] resonances were assigned and chemical shift changes monitored upon titration with Cd(2+). In addition, the two uridines flanking the branch-point, U19 and U21 were specifically thioated by chemical synthesis (thio-U19-D6-27 and thio-U19/U21-D6-27), enabling us to study Cd(2+) binding at the R P-, as well as the S P- position of the corresponding phosphate oxygens. Our studies reveal that both non-bridging phosphate oxygens of U19 are involved in metal ion coordination, whereas only the major groove phosphate oxygen of U21 is influenced. Together with NOE data of a hexaamminecobalt(III) titration, this suggests a single metal ion binding site at the GU wobble pair above the branch point in the major groove of D6 of this group II intron ribozyme.

-	~~Authors~~:	+	Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding.,Erat MC, Besic E, Oberhuber M, Johannsen S, Sigel RKO J Biol Inorg Chem. 2017 Dec 7. pii: 10.1007/s00775-017-1519-3. doi:, 10.1007/s00775-017-1519-3. PMID:29218637<ref>PMID:29218637</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6ez0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Besic, E]]
		+	[[Category: Erat, M C]]
		+	[[Category: Johannsen, S]]
		+	[[Category: Oberhuber, M]]
		+	[[Category: Sigel, R K.O]]
		+	[[Category: Rna]]
		+	[[Category: Thiophosphate group ii intron branch-adenosine hairpin tetraloop]]

OCA: Protected "6ez0" [edit=sysop:move=sysop]

2017-11-22T06:43:36Z

Protected "6ez0" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:43, 22 November 2017

OCA: New page: '''Unreleased structure''' The entry 6ez0 is ON HOLD Authors: Description: Category: Unreleased Structures

2017-11-22T06:43:35Z

New page: '''Unreleased structure''' The entry 6ez0 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ez0 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]