4TS0

Crystal structure of the Spinach RNA aptamer in complex with DFHBI, barium ions

Summary for 4TS0

• Entry DOI: 10.2210/pdb4ts0/pdb
• Related PRD ID: PRD_900003
• Descriptor: Spinach RNA aptamer, bimolecular construct, beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose, POTASSIUM ION, ... (7 entities in total)
• Functional Keywords: aptamer, fluorescence, g-quadruplex, rna
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 31765.24

Authors

Warner, K.D.,Chen, M.C.,Song, W.,Strack, R.L.,Thorn, A.,Jaffrey, S.R.,Ferre-D'Amare, A.R. (deposition date: 2014-06-18, release date: 2014-07-23, Last modification date: 2023-12-27)

Primary citation

Warner, K.D.,Chen, M.C.,Song, W.,Strack, R.L.,Thorn, A.,Jaffrey, S.R.,Ferre-D'Amare, A.R.
Structural basis for activity of highly efficient RNA mimics of green fluorescent protein.
Nat.Struct.Mol.Biol., 21:658-663, 2014

PubMed Abstract: GFP 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.

PubMed: 25026079
DOI: 10.1038/nsmb.2865

Experimental method

X-RAY DIFFRACTION (2.8 Å)