Extended Data Fig. 4. Functionally-important contacts in the B^AQR spliceosome.

a–f, Interactions between PRP2, PRP8, SF3B1, CWC22 and SKIP. Interacting distances corresponding to polar and hydrophobic contacts are indicated as dashed lines. g, Overview of PRP2 and the composite molecular brake. PRP2’s conserved domains are color-coded. HB – helix-bundle; OB – oligonucleotide/oligosaccharide- binding fold; WH – winged-helix. h, Interactions between PPIL4, SKIP, and PRP2. Residues involved in contacts are depicted as spheres and shown in the same color as their interacting partner. i, Interactions between the wedge element of SKIP and PRP2^core. j, The wedge element of SKIP appears to lock the RecA domains of PRP2. The ADP molecule is modeled by superposition with Ct PRP2 (PDB 6zm2) and is shown for the sake of orientation. k, Superposition between human PRP2 in the open conformation (observed in B^AQR) and Ct PRP2 in the closed conformation (colored in teal) (PDB 6zm2). Equivalent residues of PRP2 interacting with SKIP in B^AQR are shown for Ct PRP2. Structures from panels i and k are depicted in the same orientation. The red arrow indicates the movement of the RecA2-like domain during the helicase transition from the open to the closed conformation. l, Genetic interactions from yeast mapped on the structure of human B^AQR. The cold-sensitive allele of Prp2p^Q548N genetically interacts with the D450G and V502F substitutions of Hsh155p. Residues involved in genetic interactions in yeast (blue) are depicted as spheres and mapped on the B^AQR model. m-o, Structural superposition of the human (Hs) and budding yeast (Sc) MA3 domain of CWC22, composed from HEAT repeats. The 10^th HEAT repeat (residues 454–491) of Cwc22p is required for the productive function of yeast Prp2p and interacts with the “hook” motif of PRP2^NTD and BUD13 in B^AQR. This suggests that Prp2p, Cwc22p, and Bud13p may interact in a similar fashion in budding yeast spliceosomes, thus explaining the functional connection between Prp2p and Cwc22p. Note that human CWC22 residues that interact with PRP2 and BUD13 are conserved in budding yeast Cwc22p (shown in n and o). The protein subunits, U2 snRNA and the pre-mRNA substrate are colored and labeled.