6db9: Difference between revisions

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'''Unreleased structure'''


The entry 6db9 is ON HOLD  until Paper Publication
==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]] 2.02&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6db9]] is a 3 chain structure. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB9 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6db9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db9 OCA], [http://pdbe.org/6db9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6db9 RCSB], [http://www.ebi.ac.uk/pdbsum/6db9 PDBsum], [http://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.


Authors: Shao, Y., Shelke, S.A., Laski, A., Piccirilli, J.A.
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>


Description: Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Shelke, S.A]]
<div class="pdbe-citations 6db9" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Laski, A]]
[[Category: Laski, A]]
[[Category: Piccirilli, J A]]
[[Category: Shao, Y]]
[[Category: Shao, Y]]
[[Category: Piccirilli, J.A]]
[[Category: Shelke, S A]]
[[Category: Dir]]
[[Category: Fab]]
[[Category: Fluorescent aptamer]]
[[Category: Rna]]
[[Category: Rna-immune system complex]]
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