6E8S
Structure of the iMango-III aptamer bound to TO1-Biotin
Summary for 6E8S
| Entry DOI | 10.2210/pdb6e8s/pdb |
| Descriptor | iMango-III aptamer, 4-[(3-{2-[(2-methoxyethyl)amino]-2-oxoethyl}-1,3-benzothiazol-3-ium-2-yl)methyl]-1-methylquinolin-1-ium, POTASSIUM ION, ... (7 entities in total) |
| Functional Keywords | aptamer, fluorescence, rna, g-quadruplex |
| Biological source | synthetic construct |
| Total number of polymer chains | 2 |
| Total formula weight | 25882.81 |
| Authors | Trachman, R.J.,Ferre-D'Amare, A.R. (deposition date: 2018-07-31, release date: 2019-04-17, Last modification date: 2024-03-13) |
| 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 Cited by 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: 30992561DOI: 10.1038/s41589-019-0267-9 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.35 Å) |
Structure validation
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