6db9: Difference between revisions
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New page: '''Unreleased structure''' The entry 6db9 is ON HOLD Authors: Shao, Y., Shelke, S.A., Lask, A., Piccirilli, J.A. Description: Structural basis for promiscuous binding and activation of... |
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==Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer== | |||
<StructureSection load='6db9' size='340' side='right'caption='[[6db9]], [[Resolution|resolution]] 2.02Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6db9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DB9 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.025Å</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=6db9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db9 OCA], [https://pdbe.org/6db9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6db9 RCSB], [https://www.ebi.ac.uk/pdbsum/6db9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6db9 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO3 bound forms of DIR2s at 2.0 A and 1.8 A resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO3 fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO3, and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure. | |||
Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif.,Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA Nat Commun. 2018 Oct 31;9(1):4542. doi: 10.1038/s41467-018-06942-3. PMID:30382099<ref>PMID:30382099</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6db9" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Synthetic construct]] | |||
[[Category: Laski A]] | |||
[[Category: Piccirilli JA]] | |||
[[Category: Shao Y]] | |||
[[Category: Shelke SA]] | |||
