Structural basis for conformational equilibrium of the catalytic spliceosome

The catalytic spliceosome exists in equilibrium between the branching (B*/C) and exon ligation (C*/P) conformations. Here we present the electron cryo-microscopy reconstruction of the Saccharomyces cerevisiae C-complex spliceosome at 2.8 A resolution and identify a novel C-complex intermediate (Ci) that elucidates the molecular basis for this equilibrium. In the Ci conformation, the exon-ligation factors Prp18 and Slu7 are already bound before ATP hydrolysis by Prp16, which destabilises the branching conformation. Biochemical assays suggest these pre-bound factors prime C complex for conversion to C* by Prp16. A complete model of the Prp19-complex (NTC) shows how branching factors Yju2 and Isy1 bind the NTC before branching. Prp16 remodels Yju2 binding after branching, allowing Yju2 to remain associated with the C* complex to promote exon ligation. Our results explain how Prp16 action modulates dynamic binding of step-specific factors to alternatively stabilise the C or C* conformation and establish equilibrium of the catalytic spliceosome.