6DB8
Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer
Summary for 6DB8
| Entry DOI | 10.2210/pdb6db8/pdb |
| Descriptor | Fab-Heavy chain, RNA (60-MER), Fab-Light chain, ... (5 entities in total) |
| Functional Keywords | fluorescent aptamer, fab, dir, rna, rna-immune system complex, rna/immune system |
| Biological source | synthetic construct More |
| Total number of polymer chains | 3 |
| Total formula weight | 67525.16 |
| Authors | Shao, Y.,Shelke, S.A.,Laski, A.,Piccirilli, J.A. (deposition date: 2018-05-02, release date: 2018-11-14, Last modification date: 2024-11-06) |
| Primary citation | Shelke, S.A.,Shao, Y.,Laski, A.,Koirala, D.,Weissman, B.P.,Fuller, J.R.,Tan, X.,Constantin, T.P.,Waggoner, A.S.,Bruchez, M.P.,Armitage, B.A.,Piccirilli, J.A. Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. Nat Commun, 9:4542-4542, 2018 Cited by PubMed Abstract: The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO bound forms of DIR2s at 2.0 Å and 1.8 Å resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure. PubMed: 30382099DOI: 10.1038/s41467-018-06942-3 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.86541345549 Å) |
Structure validation
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