signaling phospholipid PIP₃ creates a new interaction surface on the nuclear receptor SF-1

Significance We previously reported that lipids PI(4,5)P ₂ (PIP ₂) and PI(3,4,5)P ₃ (PIP ₃) bind NR5A nuclear receptors to regulate their activity. Here, the crystal structures of PIP ₂ and PIP ₃ bound to NR5A1 (SF-1) define a new interaction surface that is organized by the solvent-exposed PIP ₙ headgroups. We find that stabilization by the PIP ₃ ligand propagates a signal that increases coactivator recruitment to SF-1, consistent with our earlier work showing that PIP ₃ increases SF-1 activity. This newly created surface harbors a cluster of human mutations that lead to endocrine disorders, thus explaining how these puzzling mutations cripple SF-1 activity. We propose that this new surface acts as a PIP ₃-regulated interface between SF-1 and coregulatory proteins, analogous to the function of membrane-bound phosphoinositides. The signaling phosphatidylinositol lipids PI(4,5)P ₂ (PIP ₂) and PI(3,4,5)P ₃ (PIP ₃) bind nuclear receptor 5A family (NR5As), but their regulatory mechanisms remain unknown. Here, the crystal structures of human NR5A1 (steroidogenic factor-1, SF-1) ligand binding domain (LBD) bound to PIP ₂ and PIP ₃ show the lipid hydrophobic tails sequestered in the hormone pocket, as predicted. However, unlike classic nuclear receptor hormones, the phosphoinositide head groups are fully solvent-exposed and complete the LBD fold by organizing the receptor architecture at the hormone pocket entrance. The highest affinity phosphoinositide ligand PIP ₃ stabilizes the coactivator binding groove and increases coactivator peptide recruitment. This receptor-ligand topology defines a previously unidentified regulatory protein-lipid surface on SF-1 with the phosphoinositide head group at its nexus and poised to interact with other proteins. This surface on SF-1 coincides with the predicted binding site of the corepressor DAX-1 (dosage-sensitive sex reversal, adrenal hypoplasia critical region on chromosome X), and importantly harbors missense mutations associated with human endocrine disorders. Our data provide the structural basis for this poorly understood cluster of human SF-1 mutations and demonstrates how signaling phosphoinositides function as regulatory ligands for NR5As.