Unbound primary antibodies were removed by adding and taking off 360 L wash buffer four times. The lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal and spatial control. PI3P is generated by two complexes that both contain the lipid kinase VPS34: complex II on endosomes (VPS34/VPS15/Beclin 1/UVRAG), and complex I on autophagosomes (VPS34/VPS15/Beclin 1/ATG14L). The endosomal GTPase Rab5 binds complex II, but the mechanism of VPS34 activation by Rab5 has remained elusive, and no GTPase is known to bind complex I. Sodium stibogluconate Here we show that Rab5aCGTP recruits endocytic complex II to membranes and activates it by binding between the VPS34 C2 and VPS15 WD40 domains. Electron cryotomography of complex II on Rab5a-decorated vesicles shows that the VPS34 kinase domain is released from inhibition by VPS15 and hovers over the lipid bilayer, poised for catalysis. We also show that the GTPase Rab1a, which is known to be involved in autophagy, recruits and activates the autophagy-specific complex I, but not complex II. Both Rabs bind to the same VPS34 interface but in a manner unique for each. These findings reveal how VPS34 complexes are activated on membranes by specific Rab GTPases and how they are Sodium stibogluconate recruited to unique cellular locations. for 30?min in a Ti45 rotor (Beckman Coulter). The supernatant fraction was incubated with 2?mL of IgG beads (GE Healthcare 17-0969-02) for 3.5?h. The mixture was centrifuged at 1000 C41 (DE3)), purified using Ni-NTA affinity chromatography with sonication buffer (10?mM Tris-HCl pH 8.0, 100?mM NaCl, 10?mM imidazole), 1 Complete EDTA-free Protease Inhibitor Cocktail Tablet (Roche, 11873580001), 0.1?mg/mL DNaseI, and 50?mL BugBuster (Novogen 70584), washed with Ni A1 buffer (20?mM Tris pH 8.0, 300?mM NaCl, 10?mM imidazole, 2?mM -mercaptoethanol), and Ni A2 buffer (20?mM Tris pH 8.0, 100?mM NaCl, 10?mM imidazole, 2?mM -mercaptoethanol), and eluted with an imidazole gradient with about 80?mL of Ni B1 buffer (20?mM Tris pH 8.0, 100?mM NaCl, 300?mM imidazole, 2?mM -mercaptoethanol). The His6 tag was cleaved with TEV protease (made in house) and incubated overnight with gentle rocking at 4?C, followed by purification on a HiTrap heparin column. Sodium stibogluconate The column was washed with 20?mL HA buffer (20?mM HEPES pH 8.0, 100?mM NaCl, 2?mM DTT), and the sample was eluted with 100?mL HB buffer (20?mM HEPES pH 8.0, 2?mM DTT, 1?M NaCl). The protein was further purified by gel filtration in 20?mM HEPES pH 8.0, 100?mM NaCl, 2?mM DTT. The peak fractions were pooled and concentrated to 5.2?mg/mL (51?M). Purification of p40-PX domain Purification and labelling of the p40-PX domain were described previously21. In brief, a plasmid pYO1125 was expressed in bacteria (C41 (DE3)), sonicated in lysis buffer (20?mM HEPES pH 8.0, 200?mM NaCl, 1?mM TCEP, 0.05?L/mL universal nuclease (ThermoFisher, 88702), 0.5?mg/mL lysozyme (MP Biomedicals, 195303)), affinity-purified with Glutathione Sepharose resin, washed with 100?mL wash buffer (20?mM HEPES pH 8.0, 300?mM NaCl, 1?mM TCEP) and 100?mL TEV buffer (20?mM HEPES pH 8.0, 200?mM NaCl, 1?mM TCEP). The N-terminal GST tag was cleaved Sodium stibogluconate with TEV protease and incubated overnight with gentle rocking at 4?C. The elution fractions were collected and concentrated in a 10000 MWCO Amicon Ultra15 concentrator (Millipore, UFC901024). The concentrated protein was further purified by gel filtration on a Superdex 75 CLTB 16/60 column (GE Healthcare 17-1068-01), in a buffer containing 20?mM HEPES pH 8.0, 200?mM KCl, 1?mM TCEP. The peak fractions were pooled and concentrated to 23.5?mg/mL (1.35?mM). The purified PX domain was labelled using AF647 C2 Maleimide kit (Life Technologies, A20347), and the labelled protein was purified using a heparin column. Purification of human Rab5a For the human Rab5a construct that was used for maleimide labelling, a WT Rab5a (1C212) fragment was mutated into Q79L, also surface-exposed cysteines were mutated to serines (C19S-C63S) so that one cysteine was left at the C terminus of the protein (plasmid pOP823 Sodium stibogluconate His-SUMO-Rab5a(1C212)-Q79L-C19S-C63S). Protein was overexpressed in C41(DE3)RIPL purified by Ni-NTA FF columns (GE Healthcare 17-5255-01), followed by the removal of the His-tag with SUMO protease, dialysis overnight (10?kDa MWCO, SnakeSkin? ThermoFisher) and another passage.