2n3r: Difference between revisions
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==NMR structure of the II-III-VI three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement== | ==NMR structure of the II-III-VI three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement== | ||
<StructureSection load='2n3r' size='340' side='right'caption='[[2n3r | <StructureSection load='2n3r' size='340' side='right'caption='[[2n3r]]' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2n3r]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N3R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N3R FirstGlance]. <br> | <table><tr><td colspan='2'>[[2n3r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N3R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N3R 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">Solution NMR</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=2n3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n3r OCA], [https://pdbe.org/2n3r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n3r RCSB], [https://www.ebi.ac.uk/pdbsum/2n3r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n3r 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=2n3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n3r OCA], [https://pdbe.org/2n3r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n3r RCSB], [https://www.ebi.ac.uk/pdbsum/2n3r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n3r ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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</div> | </div> | ||
<div class="pdbe-citations 2n3r" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 2n3r" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Ribozyme 3D structures|Ribozyme 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bonneau | [[Category: Neurospora crassa]] | ||
[[Category: Girard | [[Category: Bonneau E]] | ||
[[Category: Legault | [[Category: Girard N]] | ||
[[Category: Lemieux | [[Category: Legault P]] | ||
[[Category: Lemieux S]] | |||
Revision as of 21:57, 29 November 2023
NMR structure of the II-III-VI three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancementNMR structure of the II-III-VI three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement
Structural highlights
Publication Abstract from PubMedAs part of an effort to structurally characterize the complete Neurospora VS ribozyme, NMR solution structures of several subdomains have been previously determined, including the internal loops of domains I and VI, the I/V kissing-loop interaction and the III-IV-V junction. Here, we expand this work by determining the NMR structure of a 62-nucleotide RNA (J236) that encompasses the VS ribozyme II-III-VI three-way junction and its adjoining stems. In addition, we localize Mg2+-binding sites within this structure using Mn2+-induced paramagnetic relaxation enhancement. The NMR structure of the J236 RNA displays a family C topology with a compact core stabilized by continuous stacking of stems II and III, a cis WC/WC G*A base pair, two base triples and two Mg2+ ions. Moreover, it reveals a remote tertiary interaction between the adenine bulges of stems II and VI. Additional NMR studies demonstrate that both this bulge-bulge interaction and Mg2+ ions are critical for the stable folding of the II-III-VI junction. The NMR structure of the J236 RNA is consistent with biochemical studies on the complete VS ribozyme, but not with biophysical studies performed with a minimal II-III-VI junction that does not contain the II-VI bulge-bulge interaction. Together with previous NMR studies, our findings provide important new insights into the three-dimensional architecture of this unique ribozyme. The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure.,Bonneau E, Girard N, Lemieux S, Legault P RNA. 2015 Jun 29. PMID:26124200[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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