6xur - Revision history

OCA at 13:13, 24 January 2024

OCA — Wed, 24 Jan 2024 13:13:08 GMT

←Older revision		Revision as of 13:13, 24 January 2024
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	<StructureSection load='6xur' size='340' side='right'caption='[[6xur]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='6xur' size='340' side='right'caption='[[6xur]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xur]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XUR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xur]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XUR 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]] 1.1Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=O2Z:'>O2Z</scene></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>, <scene name='pdbligand=O2Z:[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-diazanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxyphosphinic+acid'>O2Z</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=6xur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xur OCA], [https://pdbe.org/6xur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xur RCSB], [https://www.ebi.ac.uk/pdbsum/6xur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xur 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=6xur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xur OCA], [https://pdbe.org/6xur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xur RCSB], [https://www.ebi.ac.uk/pdbsum/6xur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xur ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brillet, K]]	+	[[Category: Synthetic construct]]
-	[[Category: Ennifar, E]]	+	[[Category: Brillet K]]
-	[[Category: Gasser, C]]	+	[[Category: Ennifar E]]
-	[[Category: Micura, R]]	+	[[Category: Gasser C]]
-	~~[[Category: 6-hydrazino-2-aminopurine modified base]]~~	+	[[Category: Micura R]]
-	~~[[Category: Rna~~]]	+

OCA at 09:00, 5 May 2021

OCA — Wed, 05 May 2021 09:00:10 GMT

←Older revision		Revision as of 09:00, 5 May 2021
Line 3:		Line 3:
	<StructureSection load='6xur' size='340' side='right'caption='[[6xur]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='6xur' size='340' side='right'caption='[[6xur]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xur]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6XUR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xur]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XUR 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='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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=O2Z:'>O2Z</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=O2Z:'>O2Z</scene></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=6xur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xur OCA], [~~http~~://pdbe.org/6xur PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6xur RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6xur PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6xur 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=6xur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xur OCA], [https://pdbe.org/6xur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xur RCSB], [https://www.ebi.ac.uk/pdbsum/6xur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xur ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:14, 22 April 2020

OCA — Wed, 22 Apr 2020 06:14:11 GMT

←Older revision		Revision as of 06:14, 22 April 2020
Line 3:		Line 3:
	<StructureSection load='6xur' size='340' side='right'caption='[[6xur]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='6xur' size='340' side='right'caption='[[6xur]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6xur]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6XUR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xur]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XUR 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=O2Z:'>O2Z</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=O2Z:'>O2Z</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=6xur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xur OCA], [http://pdbe.org/6xur PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xur RCSB], [http://www.ebi.ac.uk/pdbsum/6xur PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xur 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=6xur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xur OCA], [http://pdbe.org/6xur PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xur RCSB], [http://www.ebi.ac.uk/pdbsum/6xur PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xur ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:45, 19 February 2020

OCA — Wed, 19 Feb 2020 06:45:45 GMT

←Older revision		Revision as of 06:45, 19 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6xur is ~~ON HOLD~~	+	==RNA dodecamer with a 6-hydrazino-2-aminopurine modified base==
		+	<StructureSection load='6xur' size='340' side='right'caption='[[6xur]], [[Resolution\|resolution]] 1.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6xur]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XUR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6XUR 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=O2Z:'>O2Z</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=6xur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xur OCA], [http://pdbe.org/6xur PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xur RCSB], [http://www.ebi.ac.uk/pdbsum/6xur PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xur ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Temporal information about cellular RNA populations is essential to understand the functional roles of RNA. We have developed hydrazine/NH 4 Cl/OsO 4 -based conversion of 6-thioguanosine (6sG)- into A'-containing RNA, where A' constitutes a 6-hydrazino purine derivative. The A' nucleoside retains the Watson-Crick base pair mode as shown by crystal structure analysis of a short palindromic duplex and thermodynamic analysis of UV-melting profiles. We further demonstrate that A' is efficiently decoded as adenosine in primer extension assays and in RNA sequencing experiments. Because 6sG is applicable to metabolic labeling of freshly synthesized RNA and because the novel conversion chemistry is fully compatible with the conversion of the frequently applied metabolic label 4-thiouridine (4sU) into C, the combination of both modified nucleosides in dual labeling set-ups enables high accuracy measurements of RNA decay. Our novel approach that we name TUC-seq DUAL uses the two modified nucleotides in subsequent pulses and their simultaneous detection. Thus, synthesis and decay of mRNA can be clearly distinguished based on the differential presence of G-to-A and U-to-C mutations. This enables mRNA life-time evaluation with unprecedented precision.

-	~~Authors: Ennifar, E~~., ~~Micura~~, R., ~~Gasser~~, C., Brillet, K.	+	Thioguanosine conversion enables mRNA life-time evaluation by RNA sequencing via double metabolic labeling.,Gasser C, Delazer I, Neuner E, Pascher K, Brillet K, Klotz S, Trixl L, Himmelstoss M, Ennifar E, Rieder D, Lusser A, Micura R Angew Chem Int Ed Engl. 2020 Jan 30. doi: 10.1002/anie.201916272. PMID:31999864<ref>PMID:31999864</ref>

-	~~Description: RNA dodecamer with~~ a 6-~~hydrazino~~-~~2-aminopurine modified base~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6xur" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Brillet, K]]
	[[Category: Ennifar, E]]		[[Category: Ennifar, E]]
	[[Category: Gasser, C]]		[[Category: Gasser, C]]
	[[Category: Micura, R]]		[[Category: Micura, R]]
-	[[Category: ~~Brillet, K~~]]	+	[[Category: 6-hydrazino-2-aminopurine modified base]]
		+	[[Category: Rna]]

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

OCA — Wed, 29 Jan 2020 13:46:30 GMT

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

←Older revision

Revision as of 13:46, 29 January 2020

OCA: New page: '''Unreleased structure''' The entry 6xur is ON HOLD Authors: Ennifar, E., Micura, R., Gasser, C., Brillet, K. Description: RNA dodecamer with a 6-hydrazino-2-aminopurine modified base...

OCA — Wed, 29 Jan 2020 13:46:28 GMT

New page: '''Unreleased structure''' The entry 6xur is ON HOLD Authors: Ennifar, E., Micura, R., Gasser, C., Brillet, K. Description: RNA dodecamer with a 6-hydrazino-2-aminopurine modified base...

New page

'''Unreleased structure'''

The entry 6xur is ON HOLD

Authors: Ennifar, E., Micura, R., Gasser, C., Brillet, K.

Description: RNA dodecamer with a 6-hydrazino-2-aminopurine modified base
[[Category: Unreleased Structures]]
[[Category: Ennifar, E]]
[[Category: Gasser, C]]
[[Category: Micura, R]]
[[Category: Brillet, K]]