6E8U

Structure of the Mango-III (A10U) aptamer bound to TO1-Biotin

Summary for 6E8U

• Entry DOI: 10.2210/pdb6e8u/pdb
• Descriptor: RNA (37-MER), MAGNESIUM ION, 4-[(3-{2,16-dioxo-20-[(3aR,4R,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium, ... (6 entities in total)
• Functional Keywords: aptamer, fluorescence, rna, g-quadruplex
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 13007.72

Authors

Trachman, R.J.,Ferre-D'Amare, A.R. (deposition date: 2018-07-31, release date: 2019-04-17, Last modification date: 2023-10-11)

Primary citation

Trachman 3rd., R.J.,Autour, A.,Jeng, S.C.Y.,Abdolahzadeh, A.,Andreoni, A.,Cojocaru, R.,Garipov, R.,Dolgosheina, E.V.,Knutson, J.R.,Ryckelynck, M.,Unrau, P.J.,Ferre-D'Amare, A.R.
Structure and functional reselection of the Mango-III fluorogenic RNA aptamer.
Nat. Chem. Biol., 15:472-479, 2019

PubMed Abstract: Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0.55). Uniquely among related aptamers, Mango-III exhibits biphasic thermal melting, characteristic of molecules with tertiary structure. We report crystal structures of TO1-Biotin complexes of Mango-III, a structure-guided mutant Mango-III(A10U), and a functionally reselected mutant iMango-III. The structures reveal a globular architecture arising from an unprecedented pseudoknot-like connectivity between a G-quadruplex and an embedded non-canonical duplex. The fluorophore is restrained into a planar conformation by the G-quadruplex, a lone, long-range trans Watson-Crick pair (whose A10U mutation increases quantum yield to 0.66), and a pyrimidine perpendicular to the nucleobase planes of those motifs. The improved iMango-III and Mango-III(A10U) fluoresce ~50% brighter than enhanced green fluorescent protein, making them suitable tags for live cell RNA visualization.

PubMed: 30992561
DOI: 10.1038/s41589-019-0267-9

Experimental method

X-RAY DIFFRACTION (1.55 Å)