Structure of the complete human TSC:WIPI3 lysosomal recruitment complex

Tuberous sclerosis complex (TSC) turns off cell growth in response to energy stress by inhibiting the master kinase mechanistic target of rapamycin complex (mTORC1). TSC hydrolyzes RAS homolog-mTORC1 binding (RHEB) from its GTP-bound to GDP-bound state, preventing the allosteric activation of mTORC1. Loss-offunction TSC mutations hyperactivate mTORC1 resulting in the common genetic disorder TSC characterized by excess cell growth and tumor formation. Here we overcome a high degree of continuous conformational heterogeneity to determine the 2.9 Å cryo-electron microscopy (cryo-EM) structure of the complete human TSC in complex with the lysosomal recruitment factor WIPI3. TSC forms an elongated 40 nm wing-like structure with a core HEAT-repeat scaffold formed by a TSC2 dimer joined centrally by the juxtaposition of two catalytic domains. The TSC1 coil-coil dimer runs across the TSC2 surface, forming a previously undetected N-terminal TSC1 dimer that clamps onto the core scaffold on a single TSC wing. Structural and biochemical analysis reveals a novel phosphatidylinositol phosphate (PIP)-binding pocket in the TSC1 dimer interface that specifically binds singularly phosphorylated PIPs. WD repeat domain phosphoinositide-interacting-protein-3 (WIPI3) binds to the extreme tip of the complex through a conserved motif in TSC1, providing a second membrane anchor point for TSC lysosomal recruitment. The TSC:WIPI3 complex helps explain how TSC lysosomal recruitment proteins coordinate with endolysosomal phosphoinositide-signaling networks to regulate TSC localization, RHEB hydrolysis, and mTORC1 inhibition. More broadly, the high-resolution structure of the complete human TSC identifies novel mutational hotspots that unravel crucial new mechanisms of TSC dysregulation in disease.