Schematic of BS binding by the U2 snRNP. (A) SF3a, SNRPA1, and SNRPB2 are omitted in this schematic. No structure of the U2 snRNP has so far shown stem–loop I, and therefore it is omitted as well. (i) The 12S U2 snRNP is created in a lengthy biogenesis process. (ii) The U2 snRNA can toggle between the IIc and IIa conformations (Rodgers et al. 2016). (iii) Association of the 12S U2 snRNP with the DDX42-bound SF3b complex and SF3a (Yang et al. 2023), possibly mediated by DDX42, forms the pre-17S U2 snRNP and stabilizes the IIa conformation (Yang et al. 2023). Through SF3B1ULM1-5, the free SF3b may already be bound to proteins like HTATSF1, which bind U2 snRNA (Tholen et al. 2022). (iv) DDX42 is displaced by DDX46 to form the DDX46-associated 17S U2 snRNP (Zhang et al. 2020, 2024; Tholen et al. 2022). (v) When the U2 snRNP is recruited to the transcript, the BSL may probe pre-mRNA for complementary sequences. [vi(a)] If complementary sequences are present, ATP hydrolysis by DDX46 removes HTATSF1, allowing the branch helix to extend, and the SF3A2 ZnF domain stabilizes it in a stalled pre-A complex (Cretu et al. 2021). [vi(b)] If DDX46 ATP hydrolysis and HTATSF1 removal occurs before formation of a toehold between BS and U2 snRNA, branch helix formation could compete with self-annealing of the U2 snRNA into a BMSL structure, which may be recycled into the 12S U2 snRNP (Tholen et al. 2022). (vii) The branch helix is fully formed in the pre-A complex, but the BP-A is not bound in its pocket. (viii) Once the bulged-out BP-A binds the pocket, SF3B1 transitions into a half-closed state, and DDX46 dissociates. SF3B6/p14 binds the U2 snRNA to SF3B1, stabilizing the branch helix. (ix) Complex A binds the U4/U6.U5 tri-snRNP to complete the assembly stage of the spliceosome. (x) Following catalysis of the splicing reaction, 12S U2 snRNP is released, allowing recycling of the U2 snRNP. (B) Possible mechanism of DHX15-mediated disassembly of A complexes or nonproductive intermediate states of BS binding (Zhang et al. 2023).
