2pn9 - Revision history

OCA at 07:05, 1 May 2024

OCA — Wed, 01 May 2024 07:05:04 GMT

←Older revision		Revision as of 07:05, 1 May 2024
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [https://pdbe.org/2pn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [https://www.ebi.ac.uk/pdbsum/2pn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pn9 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=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [https://pdbe.org/2pn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [https://www.ebi.ac.uk/pdbsum/2pn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pn9 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The trans-activating responsive (TAR) RNA element located in the 5' untranslated region of the HIV-1 genome is a 57-nt imperfect stem-loop essential for the viral replication. TAR regulates transcription by interacting with both viral and cellular proteins. RNA hairpin aptamers specific for TAR were previously identified by in vitro selection [Duconge,F. and Toulme,J.J. (1999) In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1. RNA, 5, 1605-1614]. These aptamers display a 5'-GUCCCAGA-3' consensus apical loop, partially complementary to the TAR one, leading to the formation of a TAR-aptamer kissing complex. The conserved GA combination (underlined in the consensus sequence) has been shown to be crucial for the formation of a highly stable complex. To improve the nuclease resistance of the aptamer and to increase its affinity for TAR, locked nucleic acid (LNA) nucleotides were introduced in the aptamer apical loop. LNA are nucleic acids analogues that contain a 2'-O,4'-C methylene linkage and that raise the thermostablity of duplexes. We solved the NMR solution structure of the TAR-LNA-modified aptamer kissing complex. Structural analysis revealed the formation of a non-canonical G*A pair leading to increased stacking at the stem-loop junction. Our data also showed that the introduction of LNA residues provides an enhanced stability while maintaining a normal Watson-Crick base pairing with a loop-loop conformation close to an A-type.
-
-	NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer.,Lebars I, Richard T, Di Primo C, Toulme JJ Nucleic Acids Res. 2007;35(18):6103-14. Epub 2007 Sep 3. PMID:17768146<ref>PMID:17768146</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2pn9" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:40, 13 December 2023

OCA — Wed, 13 Dec 2023 16:40:07 GMT

←Older revision		Revision as of 16:40, 13 December 2023
Line 1:		Line 1:

	==NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA modified aptamer==		==NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA modified aptamer==
-	<StructureSection load='2pn9' size='340' side='right'caption='[[2pn9~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='2pn9' size='340' side='right'caption='[[2pn9]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</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=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [https://pdbe.org/2pn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [https://www.ebi.ac.uk/pdbsum/2pn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pn9 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=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [https://pdbe.org/2pn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [https://www.ebi.ac.uk/pdbsum/2pn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pn9 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lebars, I~~]]	+	[[Category: Di Primo C]]
-	[[Category: ~~Primo, C Di~~]]	+	[[Category: Lebars I]]
-	[[Category: Richard, T]]	+	[[Category: Richard T]]
-	[[Category: Toulme, J J]]	+	[[Category: Toulme J-J]]
-	~~[[Category: Aptamer]]~~	+
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Kissing]]~~	+
-	~~[[Category: Lna]]~~	+
-	~~[[Category: Locked nucleic acid]]~~	+
-	~~[[Category: Nmr]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Tar~~]]	+

OCA at 07:46, 9 March 2022

OCA — Wed, 09 Mar 2022 07:46:35 GMT

←Older revision		Revision as of 07:46, 9 March 2022
Line 3:		Line 3:
	<StructureSection load='2pn9' size='340' side='right'caption='[[2pn9]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2pn9' size='340' side='right'caption='[[2pn9]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</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=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [~~http~~://pdbe.org/2pn9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pn9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pn9 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=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [https://pdbe.org/2pn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [https://www.ebi.ac.uk/pdbsum/2pn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pn9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:56, 3 June 2020

OCA — Wed, 03 Jun 2020 06:56:26 GMT

←Older revision		Revision as of 06:56, 3 June 2020
Line 1:		Line 1:

	==NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA modified aptamer==		==NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA modified aptamer==
-	<StructureSection load='2pn9' size='340' side='right' caption='[[2pn9]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>	+	<StructureSection load='2pn9' size='340' side='right'caption='[[2pn9]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</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=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [http://pdbe.org/2pn9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [http://www.ebi.ac.uk/pdbsum/2pn9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pn9 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=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [http://pdbe.org/2pn9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [http://www.ebi.ac.uk/pdbsum/2pn9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pn9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lebars, I]]		[[Category: Lebars, I]]
	[[Category: Primo, C Di]]		[[Category: Primo, C Di]]

OCA at 08:14, 29 August 2018

OCA — Wed, 29 Aug 2018 08:14:15 GMT

←Older revision		Revision as of 08:14, 29 August 2018
Line 1:		Line 1:
		+
	==NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA modified aptamer==		==NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA modified aptamer==
	<StructureSection load='2pn9' size='340' side='right' caption='[[2pn9]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2pn9' size='340' side='right' caption='[[2pn9]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</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=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [http://pdbe.org/2pn9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [http://www.ebi.ac.uk/pdbsum/2pn9 PDBsum]</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=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [http://pdbe.org/2pn9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [http://www.ebi.ac.uk/pdbsum/2pn9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pn9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:32, 9 September 2015

OCA — Wed, 09 Sep 2015 22:32:49 GMT

←Older revision		Revision as of 22:32, 9 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</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=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [http://www.ebi.ac.uk/pdbsum/2pn9 PDBsum]</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=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [http://pdbe.org/2pn9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [http://www.ebi.ac.uk/pdbsum/2pn9 PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2pn9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:06, 3 January 2015

OCA — Sat, 03 Jan 2015 21:06:29 GMT

←Older revision		Revision as of 21:06, 3 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</scene></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [http://www.ebi.ac.uk/pdbsum/2pn9 PDBsum]</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=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [http://www.ebi.ac.uk/pdbsum/2pn9 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Lebars, I.]]	+	[[Category: Lebars, I]]
-	[[Category: Primo, C Di.]]	+	[[Category: Primo, C Di]]
-	[[Category: Richard, T.]]	+	[[Category: Richard, T]]
-	[[Category: Toulme, J J.]]	+	[[Category: Toulme, J J]]
	[[Category: Aptamer]]		[[Category: Aptamer]]
	[[Category: Hiv-1]]		[[Category: Hiv-1]]

OCA: Protected "2pn9" [edit=sysop:move=sysop]

OCA — Mon, 09 Jun 2014 06:45:21 GMT

Protected "2pn9" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:45, 9 June 2014

OCA at 06:45, 9 June 2014

OCA — Mon, 09 Jun 2014 06:45:19 GMT

←Older revision		Revision as of 06:45, 9 June 2014
Line 1:		Line 1:
-	{~~{Seed}~~}	+	==NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA modified aptamer==
-	[[~~Image~~:2pn9.~~png\|left\|200px~~]]	+	<StructureSection load='2pn9' size='340' side='right' caption='[[2pn9]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2pn9]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PN9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=10C:4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA-L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE'>10C</scene>, <scene name='pdbligand=LCA:[(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>LCA</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pn9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pn9 RCSB], [http://www.ebi.ac.uk/pdbsum/2pn9 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The trans-activating responsive (TAR) RNA element located in the 5' untranslated region of the HIV-1 genome is a 57-nt imperfect stem-loop essential for the viral replication. TAR regulates transcription by interacting with both viral and cellular proteins. RNA hairpin aptamers specific for TAR were previously identified by in vitro selection [Duconge,F. and Toulme,J.J. (1999) In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for the TAR RNA element of HIV-1. RNA, 5, 1605-1614]. These aptamers display a 5'-GUCCCAGA-3' consensus apical loop, partially complementary to the TAR one, leading to the formation of a TAR-aptamer kissing complex. The conserved GA combination (underlined in the consensus sequence) has been shown to be crucial for the formation of a highly stable complex. To improve the nuclease resistance of the aptamer and to increase its affinity for TAR, locked nucleic acid (LNA) nucleotides were introduced in the aptamer apical loop. LNA are nucleic acids analogues that contain a 2'-O,4'-C methylene linkage and that raise the thermostablity of duplexes. We solved the NMR solution structure of the TAR-LNA-modified aptamer kissing complex. Structural analysis revealed the formation of a non-canonical G*A pair leading to increased stacking at the stem-loop junction. Our data also showed that the introduction of LNA residues provides an enhanced stability while maintaining a normal Watson-Crick base pairing with a loop-loop conformation close to an A-type.

-	<!--	+	NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer.,Lebars I, Richard T, Di Primo C, Toulme JJ Nucleic Acids Res. 2007;35(18):6103-14. Epub 2007 Sep 3. PMID:17768146<ref>PMID:17768146</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2pn9"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_2pn9\| PDB=2pn9 \| SCENE= }}~~	+

-	~~===NMR structure of~~ a ~~kissing complex formed between the TAR RNA element~~ of ~~HIV-1 and a LNA modified aptamer===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_17768146}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 17768146 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_17768146}}~~	+
-		+
-	==~~About this Structure~~==	+
-	~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA].~~	+
-		+
-	~~==Reference==~~	+
-	NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer., Lebars I, Richard T, Di Primo C, Toulme JJ, Nucleic Acids Res. 2007;35(18):6103-14. Epub 2007 Sep 3. PMID:[http:/~~/www.ncbi.nlm.nih.gov/pubmed/17768146 17768146]~~	+
	[[Category: Lebars, I.]]		[[Category: Lebars, I.]]
	[[Category: Primo, C Di.]]		[[Category: Primo, C Di.]]
Line 36:		Line 30:
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Tar]]		[[Category: Tar]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 13:54:36 2008''

OCA at 10:54, 27 July 2008

OCA — Sun, 27 Jul 2008 10:54:40 GMT

←Older revision		Revision as of 10:54, 27 July 2008
Line 1:		Line 1:
-	[[Image:2pn9.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2pn9.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2pn9\| PDB=2pn9 \| SCENE= }}		{{STRUCTURE_2pn9\| PDB=2pn9 \| SCENE= }}

-	~~'''~~NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA modified aptamer~~'''~~	+	===NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA modified aptamer===


-	~~==Overview==~~	+	<!--
-	The trans-activating responsive (TAR) RNA element located in the 5' untranslated region of the HIV-1 genome is a 57-nt imperfect stem-loop essential for the viral replication. TAR regulates transcription by interacting with both viral and cellular proteins. RNA hairpin aptamers specific for TAR were previously identified by in vitro selection [Duconge,~~F. and Toulme~~,~~J.J. (1999) In vitro selection identifies key determinants for loop-loop interactions: RNA aptamers selective for~~ the ~~TAR RNA element of HIV-1. RNA, 5, 1605-1614]. These aptamers display a 5'-GUCCCAGA-3' consensus apical loop, partially complementary~~ to the ~~TAR one, leading to the formation of a TAR-aptamer kissing complex. The conserved GA combination~~ (~~underlined in the consensus sequence) has been shown to be crucial for the formation of a highly stable complex~~. ~~To improve the nuclease resistance of the aptamer and to increase its affinity for TAR, locked nucleic acid (LNA~~) ~~nucleotides were introduced in the aptamer apical loop. LNA are nucleic acids analogues that contain a 2'-O~~,~~4'-C methylene linkage and that raise~~ the ~~thermostablity of duplexes~~. ~~We solved the NMR solution structure of the TAR~~-~~LNA~~-modified aptamer kissing complex. Structural analysis revealed the formation of a non-canonical G*A pair leading to increased stacking at the stem-loop junction. Our data also showed that the introduction of LNA residues provides an enhanced stability while maintaining a normal Watson-Crick base pairing with a loop-loop conformation close to an A-type.	+	The line below this paragraph, {{ABSTRACT_PUBMED_17768146}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17768146 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17768146}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PN9 OCA].

	==Reference==		==Reference==
Line 32:		Line 36:
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Tar]]		[[Category: Tar]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun ~~May 4~~ 13:28:03 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 13:54:36 2008''