View source for 5ob3


==iSpinach aptamer==
<StructureSection load='5ob3' size='340' side='right'caption='[[5ob3]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ob3]] is a 1 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=5OB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OB3 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]] 2.004&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1TU:4-(3,5-DIFLUORO-4-HYDROXYBENZYL)-1,2-DIMETHYL-1H-IMIDAZOL-5-OL'>1TU</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</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=5ob3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ob3 OCA], [https://pdbe.org/5ob3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ob3 RCSB], [https://www.ebi.ac.uk/pdbsum/5ob3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ob3 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Fluorogenic RNA aptamers are short nucleic acids able to specifically interact with small molecules and strongly enhance their fluorescence upon complex formation. Among the different systems recently introduced, Spinach, an aptamer forming a fluorescent complex with the 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), is one of the most promising. Using random mutagenesis and ultrahigh-throughput screening, we recently developed iSpinach, an improved version of the aptamer, endowed with an increased folding efficiency and thermal stability. iSpinach is a shorter version of Spinach comprising five mutations whom the exact role was not deciphered yet. In this work, we co-crystallized a re-engineered version of iSpinach in complex with the DFHBI and solved the x-ray structure of the complex at 2 A resolution. Only a few mutations were required to optimize iSpinach production and crystallization, underlying the good folding capacity of the molecule. The measured fluorescence half-lives in the crystal were 60% higher than in solution. Comparisons with structures previously reported for Spinach allows shedding some light on the possible function of the different beneficial mutations carried by iSpinach.

Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI.,Fernandez-Millan P, Autour A, Ennifar E, Westhof E, Ryckelynck M RNA. 2017 Sep 22. pii: rna.063008.117. doi: 10.1261/rna.063008.117. PMID:28939697<ref>PMID:28939697</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5ob3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Autour A]]
[[Category: Fernandez-Millan P]]
[[Category: Ryckelynck M]]
[[Category: Westhof E]]