5lwj - Revision history

OCA at 18:52, 18 October 2023

2023-10-18T18:52:57Z

←Older revision		Revision as of 18:52, 18 October 2023
Line 1:		Line 1:

	==Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.==		==Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.==
-	<StructureSection load='5lwj' size='340' side='right'caption='[[5lwj~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='5lwj' size='340' side='right'caption='[[5lwj]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lwj]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LWJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LWJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lwj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LWJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene~~></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP7:N1-PROTONATED+ADENOSINE-5-MONOPHOSPHATE'>AP7</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP7:N1-PROTONATED+ADENOSINE-5-MONOPHOSPHATE'>AP7</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=5lwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lwj OCA], [~~http~~://pdbe.org/5lwj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5lwj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5lwj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5lwj 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=5lwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lwj OCA], [https://pdbe.org/5lwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lwj RCSB], [https://www.ebi.ac.uk/pdbsum/5lwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lwj ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Duchardt-Ferner, E]]	+	[[Category: Synthetic construct]]
-	[[Category: Hantke, K]]	+	[[Category: Duchardt-Ferner E]]
-	[[Category: Kreutz, C]]	+	[[Category: Hantke K]]
-	[[Category: Nasiri~~, A H~~]]	+	[[Category: Kreutz C]]
-	[[Category: Ohlenschlaeger, O]]	+	[[Category: Nasiri AH]]
-	[[Category: Weickhmann~~, A K~~]]	+	[[Category: Ohlenschlaeger O]]
-	[[Category: Woehnert, J]]	+	[[Category: Weickhmann AK]]
-	[[Category: Wolter~~, A C~~]]	+	[[Category: Woehnert J]]
-	[[Category: Wunderlich~~, C H]]~~	+	[[Category: Wolter AC]]
-	~~[[Category: Aptamer]]~~	+	[[Category: Wunderlich CH]]
-	~~[[Category: Gtp]]~~	+
-	~~[[Category: Protonated adenine]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna structure~~]]	+

OCA at 13:08, 10 May 2019

2019-05-10T13:08:29Z

←Older revision		Revision as of 13:08, 10 May 2019
Line 1:		Line 1:

	==Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.==		==Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.==
-	<StructureSection load='5lwj' size='340' side='right' caption='[[5lwj]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>	+	<StructureSection load='5lwj' size='340' side='right'caption='[[5lwj]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5lwj]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LWJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5lwj]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LWJ FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Duchardt-Ferner, E]]		[[Category: Duchardt-Ferner, E]]
	[[Category: Hantke, K]]		[[Category: Hantke, K]]

OCA at 19:07, 15 December 2016

2016-12-15T19:07:49Z

←Older revision		Revision as of 19:07, 15 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5lwj is ~~ON HOLD~~	+	==Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.==
		+	<StructureSection load='5lwj' size='340' side='right' caption='[[5lwj]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5lwj]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LWJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP7:N1-PROTONATED+ADENOSINE-5-MONOPHOSPHATE'>AP7</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=5lwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lwj OCA], [http://pdbe.org/5lwj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lwj RCSB], [http://www.ebi.ac.uk/pdbsum/5lwj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lwj ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RNA tertiary structure motifs are stabilized by a wide variety of hydrogen-bonding interactions. Protonated A and C nucleotides are normally not considered to be suitable building blocks for such motifs since their pKa values are far from physiological pH. Here, we report the NMR solution structure of an in vitro selected GTP-binding RNA aptamer bound to GTP with an intricate tertiary structure. It contains a novel kind of base quartet stabilized by a protonated A residue. Owing to its unique structural environment in the base quartet, the pKa value for the protonation of this A residue in the complex is shifted by more than 5 pH units compared to the pKa for A nucleotides in single-stranded RNA. This is the largest pKa shift for an A residue in structured nucleic acids reported so far, and similar in size to the largest pKa shifts observed for amino acid side chains in proteins. Both RNA pre-folding and ligand binding contribute to the pKa shift.

-	~~Authors: Wolter,~~ A.C., Weickhmann~~, A.K.~~, Nasiri~~, A.H.~~, Hantke, K~~., Ohlenschlaeger~~, O., Wunderlich~~, C.H.~~, Kreutz, C., Duchardt-Ferner, E~~., Woehnert~~, J.	+	A Stably Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP-Binding RNA Aptamer.,Wolter AC, Weickhmann AK, Nasiri AH, Hantke K, Ohlenschlager O, Wunderlich CH, Kreutz C, Duchardt-Ferner E, Wohnert J Angew Chem Int Ed Engl. 2016 Nov 25. doi: 10.1002/anie.201609184. PMID:27885761<ref>PMID:27885761</ref>

-	~~Description: Solution NMR structure~~ of the ~~GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Nasiri, A.H]]~~	+	<div class="pdbe-citations 5lwj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Duchardt-Ferner, E]]		[[Category: Duchardt-Ferner, E]]
-	[[Category: Kreutz, C]]
	[[Category: Hantke, K]]		[[Category: Hantke, K]]
		+	[[Category: Kreutz, C]]
		+	[[Category: Nasiri, A H]]
	[[Category: Ohlenschlaeger, O]]		[[Category: Ohlenschlaeger, O]]
		+	[[Category: Weickhmann, A K]]
	[[Category: Woehnert, J]]		[[Category: Woehnert, J]]
-	[[Category: ~~Weickhmann~~, A.K]]	+	[[Category: Wolter, A C]]
-	[[Category: ~~Wolter~~, A.C]]	+	[[Category: Wunderlich, C H]]
-	[[Category: ~~Wunderlich, C.H~~]]	+	[[Category: Aptamer]]
		+	[[Category: Gtp]]
		+	[[Category: Protonated adenine]]
		+	[[Category: Rna]]
		+	[[Category: Rna structure]]

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

2016-10-03T14:47:04Z

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

←Older revision

Revision as of 14:47, 3 October 2016

OCA: New page: '''Unreleased structure''' The entry 5lwj is ON HOLD Authors: Wolter, A.C., Weickhmann, A.K., Nasiri, A.H., Hantke, K., Ohlenschlaeger, O., Wunderlich, C.H., Kreutz, C., Duchardt-Ferner...

2016-10-03T14:47:02Z

New page: '''Unreleased structure''' The entry 5lwj is ON HOLD Authors: Wolter, A.C., Weickhmann, A.K., Nasiri, A.H., Hantke, K., Ohlenschlaeger, O., Wunderlich, C.H., Kreutz, C., Duchardt-Ferner...

New page

'''Unreleased structure'''

The entry 5lwj is ON HOLD

Authors: Wolter, A.C., Weickhmann, A.K., Nasiri, A.H., Hantke, K., Ohlenschlaeger, O., Wunderlich, C.H., Kreutz, C., Duchardt-Ferner, E., Woehnert, J.

Description: Solution NMR structure of the GTP binding Class II RNA aptamer-ligand-complex containing a protonated adenine nucleotide with a highly shifted pKa.
[[Category: Unreleased Structures]]
[[Category: Nasiri, A.H]]
[[Category: Duchardt-Ferner, E]]
[[Category: Kreutz, C]]
[[Category: Hantke, K]]
[[Category: Ohlenschlaeger, O]]
[[Category: Woehnert, J]]
[[Category: Weickhmann, A.K]]
[[Category: Wolter, A.C]]
[[Category: Wunderlich, C.H]]