RNA Induces Conformational Changes in the SF1/U2AF65 Splicing Factor Complex

Spliceosomes assemble on pre-mRNA splice sites through a series of dynamic ribonucleoprotein complexes, yet the nature of the conformational changes remains unclear. Splicing factor 1 (SF1) and U2 auxiliary factor (U2AF65) cooperatively recognize the 3′ splice site during the initial stages of pre-mRNA splicing. Here, we used small-angle X-ray scattering to compare the molecular dimensions and ab initio shape restorations of SF1 and U2AF65 splicing factors, as well as the SF1/U2AF65 complex in the absence and presence of AdML (adenovirus major late) splice site RNAs. The molecular dimensions of the SF1/U2AF65/RNA complex substantially contracted by 15 Å in the maximum dimension, relative to the SF1/U2AF65 complex in the absence of RNA ligand. In contrast, no detectable changes were observed for the isolated SF1 and U2AF65 splicing factors or their individual complexes with RNA, although slight differences in the shapes of their molecular envelopes were apparent. We propose that the conformational changes that are induced by assembly of the SF1/U2AF65/RNA complex serve to position the pre-mRNA splice site optimally for subsequent stages of splicing.

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► SAXS analyses of SF1, U2AF65, and their complexes with splice site RNAs.
► Dimensions of apo- SF1 or U2AF65 remain similar when bound to their RNA sites.
► Dimensions of the SF1/U2AF65 complex contract when bound to a 3’ splice site RNA.