5y85 - Revision history

OCA at 10:22, 27 March 2024

2024-03-27T10:22:03Z

←Older revision		Revision as of 10:22, 27 March 2024
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	<StructureSection load='5y85' size='340' side='right'caption='[[5y85]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5y85' size='340' side='right'caption='[[5y85]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y85]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y85 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Y85 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y85]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Metagenome Metagenome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y85 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y85 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 2.001Å</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=5y85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y85 OCA], [~~http~~://pdbe.org/5y85 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y85 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y85 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y85 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=5y85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y85 OCA], [https://pdbe.org/5y85 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y85 RCSB], [https://www.ebi.ac.uk/pdbsum/5y85 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y85 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Here we report on the crystal structure and cleavage assays of a four-way junctional twister-sister self-cleaving ribozyme. Notably, 11 conserved spatially separated loop nucleotides are brought into close proximity at the ribozyme core through long-range interactions mediated by hydrated Mg2+ cations. The C62-A63 step at the cleavage site adopts a splayed-apart orientation, with flexible C62 directed outwards, whereas A63 is directed inwards and anchored by stacking and hydrogen-bonding interactions. Structure-guided studies of key base, sugar, and phosphate mutations in the twister-sister ribozyme, suggest contributions to the cleavage chemistry from interactions between a guanine at the active site and the non-bridging oxygen of the scissile phosphate, a feature found previously also for the related twister ribozyme. Our four-way junctional pre-catalytic structure differs significantly in the alignment at the cleavage step (splayed-apart vs. base-stacked) and surrounding residues and hydrated Mg2+ ions relative to a reported three-way junctional pre-catalytic structure of the twister-sister ribozyme.
-
-	Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme.,Zheng L, Mairhofer E, Teplova M, Zhang Y, Ma J, Patel DJ, Micura R, Ren A Nat Commun. 2017 Oct 30;8(1):1180. doi: 10.1038/s41467-017-01276-y. PMID:29081514<ref>PMID:29081514</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5y85" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
-	*[[Ribozyme\|Ribozyme]]	+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Micura, R L~~]]	+	[[Category: Metagenome]]
-	[[Category: ~~Ren, A~~]]	+	[[Category: Micura RL]]
-	[[Category: ~~Zheng, L~~]]	+	[[Category: Ren A]]
-	[[Category: ~~Catalysis]]~~	+	[[Category: Zheng L]]
-	~~[[Category: Riboyzme]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Self-cleaving]]~~	+
-	~~[[Category: Twister-sister~~]]	+

OCA at 09:13, 21 October 2020

2020-10-21T09:13:01Z

←Older revision		Revision as of 09:13, 21 October 2020
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	==Structure-based Insights into Self-Cleavage by a Four-way Junctional Twister-Sister Ribozyme==		==Structure-based Insights into Self-Cleavage by a Four-way Junctional Twister-Sister Ribozyme==
-	<StructureSection load='5y85' size='340' side='right' caption='[[5y85]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5y85' size='340' side='right'caption='[[5y85]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y85]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y85 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y85 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y85]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y85 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Y85 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></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5y85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y85 OCA], [http://pdbe.org/5y85 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y85 RCSB], [http://www.ebi.ac.uk/pdbsum/5y85 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y85 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=5y85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y85 OCA], [http://pdbe.org/5y85 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y85 RCSB], [http://www.ebi.ac.uk/pdbsum/5y85 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y85 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 5y85" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5y85" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribozyme\|Ribozyme]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Micura, R L]]		[[Category: Micura, R L]]
	[[Category: Ren, A]]		[[Category: Ren, A]]

OCA at 07:46, 22 November 2017

2017-11-22T07:46:16Z

←Older revision		Revision as of 07:46, 22 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5y85 is ~~ON HOLD~~	+	==Structure-based Insights into Self-Cleavage by a Four-way Junctional Twister-Sister Ribozyme==
		+	<StructureSection load='5y85' size='340' side='right' caption='[[5y85]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5y85]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y85 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y85 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></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=5y85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y85 OCA], [http://pdbe.org/5y85 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y85 RCSB], [http://www.ebi.ac.uk/pdbsum/5y85 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y85 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Here we report on the crystal structure and cleavage assays of a four-way junctional twister-sister self-cleaving ribozyme. Notably, 11 conserved spatially separated loop nucleotides are brought into close proximity at the ribozyme core through long-range interactions mediated by hydrated Mg2+ cations. The C62-A63 step at the cleavage site adopts a splayed-apart orientation, with flexible C62 directed outwards, whereas A63 is directed inwards and anchored by stacking and hydrogen-bonding interactions. Structure-guided studies of key base, sugar, and phosphate mutations in the twister-sister ribozyme, suggest contributions to the cleavage chemistry from interactions between a guanine at the active site and the non-bridging oxygen of the scissile phosphate, a feature found previously also for the related twister ribozyme. Our four-way junctional pre-catalytic structure differs significantly in the alignment at the cleavage step (splayed-apart vs. base-stacked) and surrounding residues and hydrated Mg2+ ions relative to a reported three-way junctional pre-catalytic structure of the twister-sister ribozyme.

-	~~Authors: Zheng~~, L., ~~Micura~~, R~~.L.~~, Ren, A.	+	Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme.,Zheng L, Mairhofer E, Teplova M, Zhang Y, Ma J, Patel DJ, Micura R, Ren A Nat Commun. 2017 Oct 30;8(1):1180. doi: 10.1038/s41467-017-01276-y. PMID:29081514<ref>PMID:29081514</ref>

-	~~Description: Structure-based Insights into Self-Cleavage by~~ a ~~Four~~-~~way Junctional Twister~~-~~Sister Ribozyme~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5y85" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Micura, R L]]
	[[Category: Ren, A]]		[[Category: Ren, A]]
-	[[Category: Micura, R.L]]
	[[Category: Zheng, L]]		[[Category: Zheng, L]]
		+	[[Category: Catalysis]]
		+	[[Category: Riboyzme]]
		+	[[Category: Rna]]
		+	[[Category: Self-cleaving]]
		+	[[Category: Twister-sister]]

OCA: Protected "5y85" [edit=sysop:move=sysop]

2017-09-27T16:15:20Z

Protected "5y85" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:15, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y85 is ON HOLD Authors: Zheng, L., Micura, R.L., Ren, A. Description: Structure-based Insights into Self-Cleavage by a Four-way Junctional Twister...

2017-09-27T16:15:19Z

New page: '''Unreleased structure''' The entry 5y85 is ON HOLD Authors: Zheng, L., Micura, R.L., Ren, A. Description: Structure-based Insights into Self-Cleavage by a Four-way Junctional Twister...

New page

'''Unreleased structure'''

The entry 5y85 is ON HOLD

Authors: Zheng, L., Micura, R.L., Ren, A.

Description: Structure-based Insights into Self-Cleavage by a Four-way Junctional Twister-Sister Ribozyme
[[Category: Unreleased Structures]]
[[Category: Ren, A]]
[[Category: Micura, R.L]]
[[Category: Zheng, L]]