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==Crystal structure of the Spinach RNA aptamer in complex with DFHBI, barium ions== | ==Crystal structure of the Spinach RNA aptamer in complex with DFHBI, barium ions== | ||
<StructureSection load='4ts0' size='340' side='right' caption='[[4ts0]], [[Resolution|resolution]] 2.80Å' scene=''> | <StructureSection load='4ts0' size='340' side='right'caption='[[4ts0]], [[Resolution|resolution]] 2.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4ts0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TS0 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[4ts0]] is a 2 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=4TS0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TS0 FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=38E:(5Z)-5-(3,5-DIFLUORO-4-HYDROXYBENZYLIDENE)-2,3-DIMETHYL-3,5-DIHYDRO-4H-IMIDAZOL-4-ONE'>38E</scene>, <scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand= | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> | ||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=38E:(5Z)-5-(3,5-DIFLUORO-4-HYDROXYBENZYLIDENE)-2,3-DIMETHYL-3,5-DIHYDRO-4H-IMIDAZOL-4-ONE'>38E</scene>, <scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene></td></tr> | ||
<table> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ts0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ts0 OCA], [https://pdbe.org/4ts0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ts0 RCSB], [https://www.ebi.ac.uk/pdbsum/4ts0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ts0 ProSAT]</span></td></tr> | ||
</table> | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 4ts0" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: | [[Category: Chen MC]] | ||
[[Category: | [[Category: Ferre-D'Amare AR]] | ||
[[Category: | [[Category: Jaffrey SR]] | ||
[[Category: | [[Category: Song W]] | ||
[[Category: | [[Category: Strack RL]] | ||
[[Category: | [[Category: Thorn A]] | ||
[[Category: | [[Category: Warner KD]] | ||
Latest revision as of 03:47, 28 December 2023
Crystal structure of the Spinach RNA aptamer in complex with DFHBI, barium ionsCrystal structure of the Spinach RNA aptamer in complex with DFHBI, barium ions
Structural highlights
Publication Abstract from PubMedGFP and its derivatives revolutionized the study of proteins. Spinach is a recently reported in vitro-evolved RNA mimic of GFP, which as genetically encoded fusions makes possible live-cell, real-time imaging of biological RNAs without resorting to large RNA-binding protein-GFP fusions. To elucidate the molecular basis of Spinach fluorescence, we solved the cocrystal structure of Spinach bound to its cognate exogenous chromophore, showing that Spinach activates the small molecule by immobilizing it between a base triple, a G-quadruplex and an unpaired G. Mutational and NMR analyses indicate that the G-quadruplex is essential for Spinach fluorescence, is also present in other fluorogenic RNAs and may represent a general strategy for RNAs to induce fluorescence of chromophores. The structure guided the design of a miniaturized 'Baby Spinach', and it provides a foundation for structure-driven design and tuning of fluorescent RNAs. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein.,Warner KD, Chen MC, Song W, Strack RL, Thorn A, Jaffrey SR, Ferre-D'Amare AR Nat Struct Mol Biol. 2014 Jul 15. doi: 10.1038/nsmb.2865. PMID:25026079[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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