5V3F
Co-crystal structure of the fluorogenic RNA Mango
Summary for 5V3F
| Entry DOI | 10.2210/pdb5v3f/pdb |
| Descriptor | RNA (31-MER), POTASSIUM ION, 4-{[(2S)-3-{2,16-dioxo-20-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-2,3-dihydro-1,3-benzothiazol-2-yl]methyl}-1-methylquinolin-1-ium, ... (5 entities in total) |
| Functional Keywords | quadruplex fluorescent rna, rna |
| Biological source | synthetic construct |
| Total number of polymer chains | 2 |
| Total formula weight | 22428.93 |
| Authors | Trachman, R.J.,Ferre-D'Amare, A.R. (deposition date: 2017-03-07, release date: 2017-05-24, Last modification date: 2024-03-06) |
| Primary citation | Trachman, R.J.,Demeshkina, N.A.,Lau, M.W.L.,Panchapakesan, S.S.S.,Jeng, S.C.Y.,Unrau, P.J.,Ferre-D'Amare, A.R. Structural basis for high-affinity fluorophore binding and activation by RNA Mango. Nat. Chem. Biol., 13:807-813, 2017 Cited by PubMed Abstract: Genetically encoded fluorescent protein tags have revolutionized proteome studies, whereas the lack of intrinsically fluorescent RNAs has hindered transcriptome exploration. Among several RNA-fluorophore complexes that potentially address this problem, RNA Mango has an exceptionally high affinity for its thiazole orange (TO)-derived fluorophore, TO1-Biotin (K ∼3 nM), and, in complex with related ligands, it is one of the most redshifted fluorescent macromolecular tags known. To elucidate how this small aptamer exhibits such properties, which make it well suited for studying low-copy cellular RNAs, we determined its 1.7-Å-resolution co-crystal structure. Unexpectedly, the entire ligand, including TO, biotin and the linker connecting them, abuts one of the near-planar faces of the three-tiered G-quadruplex. The two heterocycles of TO are held in place by two loop adenines and form a 45° angle with respect to each other. Minimizing this angle would increase quantum yield and further improve this tool for in vivo RNA visualization. PubMed: 28553947DOI: 10.1038/nchembio.2392 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.7 Å) |
Structure validation
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