Structural Insights into Branch Site Proofreading by Human Spliceosome

Abstract Selection of the pre-mRNA branch site (BS) by U2 snRNP is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection; but the underlying mechanism remains unclear. Here we report the atomic structures of two sequential complexes leading to prespliceosome assembly: human 17S U2 snRNP and a cross-exon pre-A complex. PRP5 is anchored on 17S U2 snRNP mainly through occupation of the RNA path of SF3B1 by an acidic loop of PRP5; the helicase domain of PRP5 associates with U2 snRNA; the BS-interacting stem loop (BSL) of U2 snRNA is shielded by the splicing factor TAT-SF1, unable to engage the BS. In the pre-A complex, an initial U2/BS duplex is formed; the translocated helicase domain of PRP5 stays with U2 snRNA; the acidic loop still occupies the RNA path. The pre-A conformation is specifically stabilized by the splicing factors SF1, DNAJC8 and SF3A2. Cancer-derived mutations in SF3B1 damage its association with PRP5, compromising BS proofreading. Together, these findings reveal key insights into prespliceosome assembly and BS selection/proofreading by PRP5.