Fig. 2: Features of the Beetroot-DFAME binding site and the interprotomer interface. | Nature Communications

Fig. 2: Features of the Beetroot-DFAME binding site and the interprotomer interface.

From: Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture

Fig. 2

a View of the binding site with bound DFAME sandwiched between the T4 tetrad and the terminal A16•U38 Watson-Crick pair of P2, colored as in Fig. 1. Gray mesh depicts the |Fo | − |Fc| electron density map before building DFAME fluorophore, contoured at 3.0 standard deviations above mean peak height (σ). Yellow dashed lines denote hydrogen bonds. b Orthogonal view of a the binding site of Beetroot–DFAME from the direction of P2. c Orthogonal view of a the binding site from the direction of the interprotomer interface and with the electron density map omitted. d View of the interprotomer interface of Beetroot with the top two G-quartets tiers (T1 and T2, and t1 and t2) and the adenosine that makes interprotomer interaction (A31 and a31). The five octacoordinated K+ ions and water molecules (purple and red spheres, respectively) are depicted. Gray dashed line denotes the dimer interface. e Detail of A31 and its interaction with both protomers. f Fluorescence activation of DFAME by wild-type and A31 mutants (mean±s.d., n = 3 – n denotes independent sample replicate). g Baseline-corrected thermogram, non-linear least-squares fit, and residuals for Beetroot titration with DFAME (mean±s.d., n = 1 – n denotes independent experiment). Refer to Supplementary Fig. 5a for triplicate data.

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