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==Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop==
==Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop==
<StructureSection load='5v2r' size='340' side='right'caption='[[5v2r]], [[NMR_Ensembles_of_Models | 33 NMR models]]' scene=''>
<StructureSection load='5v2r' size='340' side='right'caption='[[5v2r]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5v2r]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V2R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V2R FirstGlance]. <br>
<table><tr><td colspan='2'>[[5v2r]] is a 2 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=5V2R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V2R FirstGlance]. <br>
</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=5v2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v2r OCA], [http://pdbe.org/5v2r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v2r RCSB], [http://www.ebi.ac.uk/pdbsum/5v2r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v2r ProSAT]</span></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5v2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v2r OCA], [https://pdbe.org/5v2r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v2r RCSB], [https://www.ebi.ac.uk/pdbsum/5v2r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v2r ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The prediction of RNA three-dimensional structure from sequence alone has been a long-standing goal. High-resolution, experimentally determined structures of simple noncanonical pairings and motifs are critical to the development of prediction programs. Here, we present the nuclear magnetic resonance structure of the (5'CCAGAAACGGAUGGA)2 duplex, which contains an 8 x 8 nucleotide internal loop flanked by three Watson-Crick pairs on each side. The loop is comprised of a central 5'AC/3'CA nearest neighbor flanked by two 3RRs motifs, a known stable motif consisting of three consecutive sheared GA pairs. Hydrogen bonding patterns between base pairs in the loop, the all-atom root-mean-square deviation for the loop, and the deformation index were used to compare the structure to automated predictions by MC-sym, RNA FARFAR, and RNAComposer.
Nuclear Magnetic Resonance Structure of an 8 x 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions.,Kauffmann AD, Kennedy SD, Zhao J, Turner DH Biochemistry. 2017 Jul 25;56(29):3733-3744. doi: 10.1021/acs.biochem.7b00201., Epub 2017 Jul 12. PMID:28700212<ref>PMID:28700212</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5v2r" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Kauffmann, A D]]
[[Category: Synthetic construct]]
[[Category: Kennedy, S D]]
[[Category: Kauffmann AD]]
[[Category: Turner, D H]]
[[Category: Kennedy SD]]
[[Category: 3rrs ga sheared pairs ac pair]]
[[Category: Turner DH]]
[[Category: Rna]]

Latest revision as of 07:28, 1 May 2024

Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop

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