Cancer-relevant Splicing Factor CAPERα Engages the Essential Splicing Factor SF3b155 in a Specific Ternary Complex

U2AF homology motifs (UHMs) mediate protein-protein interactions with U2AF ligand motifs (ULMs) of pre-mRNA splicing factors. The UHM-containing alternative splicing factor CAPER alpha regulates splicing of tumor-promoting VEGF isoforms, yet the molecular target of the CAPER alpha UHM is unknown. Here we present structures of the CAPER alpha UHM bound to a representative SF3b155 ULM at 1.7 angstrom resolution and, for comparison, in the absence of ligand at 2.2 angstrom resolution. The prototypical UHM/ULM interactions authenticate CAPER alpha as a bona fide member of the UHM family of proteins. We identify SF3b155 as the relevant ULM-containing partner of full-length CAPER alpha in human cell extracts. Isothermal titration calorimetry comparisons of the purified CAPER alpha UHM binding known ULM-containing proteins demonstrate that high affinity interactions depend on the presence of an intact, intrinsically unstructured SF3b155 domain containing seven ULM-like motifs. The interplay among bound CAPER alpha molecules gives rise to the appearance of two high affinity sites in the SF3b155 ULM-containing domain. In conjunction with the previously identified, UHM/ULM-mediated complexes of U2AF(65) and SPF45 with SF3b155, this work demonstrates the capacity of SF3b155 to offer a platform for coordinated recruitment of UHM-containing splicing factors.