6PQ7
Structure of the iMango-III fluorescent aptamer at room temperature.
Summary for 6PQ7
| Entry DOI | 10.2210/pdb6pq7/pdb |
| Related | 6E8U |
| Descriptor | RNA (37-MER), MAGNESIUM ION, ~{N}-[2-[2-[2-[2-[2-[2-[(1-methylquinolin-4-yl)methyl]-1,3-benzothiazol-3-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethyl]pentanamide, ... (4 entities in total) |
| Functional Keywords | fluorescent, rna, aptamer, xfels |
| Biological source | synthetic construct |
| Total number of polymer chains | 1 |
| Total formula weight | 12722.34 |
| Authors | Trachman III, R.J.,Ferre-D'Amare, A.R. (deposition date: 2019-07-08, release date: 2019-07-31, Last modification date: 2023-10-11) |
| Primary citation | Trachman III, R.J.,Stagno, J.R.,Conrad, C.,Jones, C.P.,Fischer, P.,Meents, A.,Wang, Y.X.,Ferre-D'Amare, A.R. Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser. Acta Crystallogr.,Sect.F, 75:547-551, 2019 Cited by PubMed Abstract: Turn-on aptamers are in vitro-selected RNAs that bind to conditionally fluorescent small molecules and enhance their fluorescence. Upon binding TO1-biotin, the iMango-III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers (over 5000-fold). This aptamer was generated by structure-guided engineering and functional reselection of the parental aptamer Mango-III. Structures of both Mango-III and iMango-III have previously been determined by conventional cryocrystallography using synchrotron X-radiation. Using an X-ray free-electron laser (XFEL), the room-temperature iMango-III-TO1-biotin co-crystal structure has now been determined at 3.0 Å resolution. This structural model, which was refined against a data set of ∼1300 diffraction images (each from a single crystal), is largely consistent with the structures determined from single-crystal data sets collected at 100 K. This constitutes a technical benchmark on the way to XFEL pump-probe experiments on fluorescent RNA-small molecule complexes. PubMed: 31397326DOI: 10.1107/S2053230X19010136 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3 Å) |
Structure validation
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