7v9e - Revision history

OCA at 19:42, 29 May 2024

2024-05-29T19:42:37Z

←Older revision		Revision as of 19:42, 29 May 2024
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	==Crystal structure of a methyl transferase ribozyme==		==Crystal structure of a methyl transferase ribozyme==
-	<StructureSection load='7v9e' size='340' side='right'caption='[[7v9e]]' scene=''>	+	<StructureSection load='7v9e' size='340' side='right'caption='[[7v9e]], [[Resolution\|resolution]] 2.30Å' 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=7V9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9E FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9E 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=7v9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9e OCA], [https://pdbe.org/7v9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9e RCSB], [https://www.ebi.ac.uk/pdbsum/7v9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9e ProSAT]</span></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]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=GUN:GUANINE'>GUN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7v9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9e OCA], [https://pdbe.org/7v9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9e RCSB], [https://www.ebi.ac.uk/pdbsum/7v9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9e ProSAT]</span></td></tr>
	</table>		</table>
		+
		+	==See Also==
		+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:54, 31 August 2022

2022-08-31T14:54:24Z

←Older revision		Revision as of 14:54, 31 August 2022
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	==Crystal structure of a methyl transferase ribozyme==		==Crystal structure of a methyl transferase ribozyme==
-	<StructureSection load='7v9e' size='340' side='right'caption='[[7v9e]]~~, [[Resolution\|resolution]] 2.30Å~~' scene=''>	+	<StructureSection load='7v9e' size='340' side='right'caption='[[7v9e]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[7v9e]] is a 1 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9E FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=GUN:GUANINE'>GUN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</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=7v9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9e OCA], [https://pdbe.org/7v9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9e RCSB], [https://www.ebi.ac.uk/pdbsum/7v9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9e ProSAT]</span></td></tr>
-	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</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=7v9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9e OCA], [https://pdbe.org/7v9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9e RCSB], [https://www.ebi.ac.uk/pdbsum/7v9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9e ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Known ribozymes in contemporary biology perform a limited range of chemical catalysis, but in vitro selection has generated species that catalyze a broader range of chemistry; yet, there have been few structural and mechanistic studies of selected ribozymes. A ribozyme has recently been selected that can catalyze a site-specific methyl transfer reaction. We have solved the crystal structure of this ribozyme at a resolution of 2.3 A, showing how the RNA folds to generate a very specific binding site for the methyl donor substrate. The structure immediately suggests a catalytic mechanism involving a combination of proximity and orientation and nucleobase-mediated general acid catalysis. The mechanism is supported by the pH dependence of the rate of catalysis. A selected methyltransferase ribozyme can thus use a relatively sophisticated catalytic mechanism, broadening the range of known RNA-catalyzed chemistry.
-
-	Structure and mechanism of a methyltransferase ribozyme.,Deng J, Wilson TJ, Wang J, Peng X, Li M, Lin X, Liao W, Lilley DMJ, Huang L Nat Chem Biol. 2022 Mar 17. pii: 10.1038/s41589-022-00982-z. doi:, 10.1038/s41589-022-00982-z. PMID:35301479<ref>PMID:35301479</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7v9e" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Deng, J]]	+	[[Category: Deng J]]
-	[[Category: Huang, L]]	+	[[Category: Huang L]]
-	[[Category: Lilley~~, D M.J]]~~	+	[[Category: Lilley DMJ]]
-	~~[[Category: Methyl transferase]]~~	+
-	~~[[Category: Riboswitch]]~~	+
-	~~[[Category: Ribozyme]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 11:18, 30 March 2022

2022-03-30T11:18:46Z

←Older revision		Revision as of 11:18, 30 March 2022
Line 1:		Line 1:

	==Crystal structure of a methyl transferase ribozyme==		==Crystal structure of a methyl transferase ribozyme==
-	<StructureSection load='7v9e' size='340' side='right'caption='[[7v9e]]' scene=''>	+	<StructureSection load='7v9e' size='340' side='right'caption='[[7v9e]], [[Resolution\|resolution]] 2.30Å' 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=7V9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7v9e]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9E 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=7v9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9e OCA], [https://pdbe.org/7v9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9e RCSB], [https://www.ebi.ac.uk/pdbsum/7v9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9e 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=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=GUN:GUANINE'>GUN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</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=7v9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9e OCA], [https://pdbe.org/7v9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9e RCSB], [https://www.ebi.ac.uk/pdbsum/7v9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9e ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Known ribozymes in contemporary biology perform a limited range of chemical catalysis, but in vitro selection has generated species that catalyze a broader range of chemistry; yet, there have been few structural and mechanistic studies of selected ribozymes. A ribozyme has recently been selected that can catalyze a site-specific methyl transfer reaction. We have solved the crystal structure of this ribozyme at a resolution of 2.3 A, showing how the RNA folds to generate a very specific binding site for the methyl donor substrate. The structure immediately suggests a catalytic mechanism involving a combination of proximity and orientation and nucleobase-mediated general acid catalysis. The mechanism is supported by the pH dependence of the rate of catalysis. A selected methyltransferase ribozyme can thus use a relatively sophisticated catalytic mechanism, broadening the range of known RNA-catalyzed chemistry.
		+
		+	Structure and mechanism of a methyltransferase ribozyme.,Deng J, Wilson TJ, Wang J, Peng X, Li M, Lin X, Liao W, Lilley DMJ, Huang L Nat Chem Biol. 2022 Mar 17. pii: 10.1038/s41589-022-00982-z. doi:, 10.1038/s41589-022-00982-z. PMID:35301479<ref>PMID:35301479</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7v9e" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Deng J]]	+	[[Category: Deng, J]]
-	[[Category: Huang L]]	+	[[Category: Huang, L]]
-	[[Category: Lilley ~~DMJ~~]]	+	[[Category: Lilley, D M.J]]
		+	[[Category: Methyl transferase]]
		+	[[Category: Riboswitch]]
		+	[[Category: Ribozyme]]
		+	[[Category: Rna]]

OCA at 11:21, 23 March 2022

2022-03-23T11:21:48Z

←Older revision		Revision as of 11:21, 23 March 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7v9e is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of a methyl transferase ribozyme==
-		+	<StructureSection load='7v9e' size='340' side='right'caption='[[7v9e]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9E 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=7v9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9e OCA], [https://pdbe.org/7v9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9e RCSB], [https://www.ebi.ac.uk/pdbsum/7v9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9e ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Deng J]]
		+	[[Category: Huang L]]
		+	[[Category: Lilley DMJ]]

OCA at 12:16, 29 December 2021

2021-12-29T12:16:33Z

←Older revision		Revision as of 12:16, 29 December 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7v9e is ON HOLD	+	The entry 7v9e is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7v9e" [edit=sysop:move=sysop]

2021-09-08T07:59:57Z

Protected "7v9e" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:59, 8 September 2021

OCA: New page: '''Unreleased structure''' The entry 7v9e is ON HOLD Authors: Description: Category: Unreleased Structures

2021-09-08T07:59:56Z

New page: '''Unreleased structure''' The entry 7v9e is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7v9e is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]