AlphaFold3 predictions of novel GLI-SUFU interfaces identify binding-defective SUFU missense variants from medulloblastoma and Gorlin syndrome patients

Abstract The tumor suppressor SUFU is a key negative regulator of oncogenic GLI transcription factors. SUFU mutations predispose to medulloblastoma and can cause Gorlin and Joubert syndromes. Limited structural information is available on the GLI-SUFU complex, contributing to the fact that the vast majority of SUFU missense variants sequenced from affected patients are of unknown clinical significance. Using AlphaFold3 and complementary computational analysis, we predicted structures of the three human GLI-SUFU complexes and the orthologous Drosophila Ci-Sufu complex, revealing previously unrecognized contact interfaces. By site-directed mutagenesis and GLI-SUFU binding assays, we validated the importance of key interface residues, many of which are mutated in familial medulloblastoma and Gorlin syndrome. These findings provide new structure-function insights into a signaling complex mutated in cancer and rare congenital diseases, and offer an expanded framework for interpreting clinically observed SUFU variants and mechanisms that tune SUFU repression. Teaser AI-powered modeling plus experimental validation reveal new GLI–SUFU interfaces linked to cancer and congenital mutations.