Extended Data Fig. 9: DV in the pre-branching state is in an active conformation.

The AGC triad and two-nt bulge of DV (red) are shown with the M1 and M2 catalytic metal ions bound (orange). Coordination of the metals is shown as yellow dashed lines. M1 and M2 are 6.4 Å apart (dashed black line) requiring DV to undergo a small conformational change to bring the metals into the proximity required for catalysis. The metal ion distance provides a rational for why the pre-branching state was captured. A black arrow indicates the nucleophilic attack performed during branching once the metal ion binding pocket tightens. In addition, both the bulged adenosine (yellow) and the scissile phosphate of U1 (green) are both in position to perform the branching reaction. The sharpened map corresponding to the pre-branching state is shown overlayed with the model to highlight the fit.