biostudies-literatureTremel SCancer Research UKDeutsche ForschungsgemeinschaftEuropean Research CouncilMedical Research CouncilWellcome Trust1564https://www.ebi.ac.uk/biostudies/studies/S-EPMC7946940biostudies-literatureUnknown12(1)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. Here we show that Rab5a-GTP 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 kinNature communicationsStructural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes.PMC7946940Sonderforschungsbereich 1035, project number 201302640Sonderforschungsbereich 1035, project B10392923329648432MC_U105184308MC_U105178783C14801/A21211103139MC_U105184326MC_U10517878MC_UP_1201/16203149Perisic OChen ZAMaslen SLLang KRappsilber JBriggs JAGMorado DRBertram JKovtun OBrandt LTLvon Wrisberg MKSkehel MTremel SOhashi YWilliams RLMunro SfalseStructural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes.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. Here we show that Rab5a-GTP 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 kin2021-01-01T00:00:00Z2021 Mar2026-05-10T03:28:50.218Z2025-02-19T00:17:40.324ZS-EPMC79469403369236010.1038/s41467-021-21695-2