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==PEMV-1 P1-P2 Frameshifting Pseudoknot, 15 Lowest Energy Structures==
==PEMV-1 P1-P2 Frameshifting Pseudoknot, 15 Lowest Energy Structures==
<StructureSection load='1kpy' size='340' side='right' caption='[[1kpy]], [[NMR_Ensembles_of_Models | 15 NMR models]]' scene=''>
<StructureSection load='1kpy' size='340' side='right'caption='[[1kpy]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1kpy]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KPY FirstGlance]. <br>
<table><tr><td colspan='2'>[[1kpy]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KPY FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CH:N3-PROTONATED+CYTIDINE-5-MONOPHOSPHATE'>CH</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kpz|1kpz]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CH:N3-PROTONATED+CYTIDINE-5-MONOPHOSPHATE'>CH</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=1kpy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpy OCA], [http://pdbe.org/1kpy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kpy RCSB], [http://www.ebi.ac.uk/pdbsum/1kpy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kpy 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=1kpy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kpy OCA], [https://pdbe.org/1kpy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kpy RCSB], [https://www.ebi.ac.uk/pdbsum/1kpy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kpy ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A hairpin-type messenger RNA pseudoknot from pea enation mosaic virus RNA1 (PEMV-1) regulates the efficiency of programmed -1 ribosomal frameshifting. The solution structure and 15N relaxation rates reveal that the PEMV-1 pseudoknot is a compact-folded structure composed almost entirely of RNA triple helix. A three nucleotide reverse turn in loop 1 positions a protonated cytidine, C(10), in the correct orientation to form an A((n-1)).C(+).G-C(n) major groove base quadruple, like that found in the beet western yellows virus pseudoknot and the hepatitis delta virus ribozyme, despite distinct structural contexts. A novel loop 2-loop 1 A.U Hoogsteen base-pair stacks on the C(10)(+).G(28) base-pair of the A(12).C(10)(+).G(28)-C(13) quadruple and forms a wedge between the pseudoknot stems stabilizing a bent and over-rotated global conformation. Substitution of key nucleotides that stabilize the unique conformation of the PEMV-1 pseudoknot greatly reduces ribosomal frameshifting efficacy.
Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot.,Nixon PL, Rangan A, Kim YG, Rich A, Hoffman DW, Hennig M, Giedroc DP J Mol Biol. 2002 Sep 20;322(3):621-33. PMID:12225754<ref>PMID:12225754</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1kpy" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Giedroc, D P]]
[[Category: Large Structures]]
[[Category: Nixon, P L]]
[[Category: Giedroc DP]]
[[Category: Frameshifting]]
[[Category: Nixon PL]]
[[Category: Luteovirus]]
[[Category: Protonated cytidine]]
[[Category: Pseudoknot]]
[[Category: Ribonucleic acid]]
[[Category: Rna]]
[[Category: Triple helix]]

Latest revision as of 06:31, 1 May 2024

PEMV-1 P1-P2 Frameshifting Pseudoknot, 15 Lowest Energy Structures

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