RABEX-5 and other exchange factors with VPS9 domains regulate endocytic trafficking through activation of the Rab family GTPases RAB5, RAB21 and RAB22. Here we report the crystal structure of the RABEX-5 catalytic core in complex with nucleotide-free RAB21, a key intermediate in the exchange reaction pathway. The structure reveals how VPS9 domain exchange factors recognize Rab GTPase substrates, accelerate GDP release and stabilize the nucleotide-free conformation. We further identify an autoinhibitory element in a predicted amphipathic helix located near the C terminus of the VPS9 domain. The autoinhibitory element overlaps with the binding site for the multivalent effector RABAPTIN-5 and potently suppresses the exchange activity of RABEX-5. Autoinhibition can be partially reversed by mutation of conserved residues on the nonpolar face of the predicted amphipathic helix or by assembly of the complex with RABAPTIN-5.The essential regulatory function of Rab GTPases in membrane trafficking, organelle biogenesis and cell growth depends on their ability to cycle between active (GTP-bound) and inactive (GDP-bound) conformations 1,2 . In the active conformation, Rab GTPases mediate selective interactions with effectors, including cargo-sorting complexes, motor proteins, tethering factors and lipid kinases, as well as proteins implicated in signal transduction, cytoskeletal dynamics and cytokinesis. The intrinsic rates of activation by nucleotide exchange and deactivation by GTP hydrolysis are slow compared with the timescale of the relevant cellular processes. Consequently, the interconversion between states is tightly regulated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs).Null and temperature-sensitive alleles of the yeast VPS9 gene result in mis-sorting of proteins targeted to the vacuole 3 . Yeast Vps9p has GEF activity for the yeast RAB5 homolog Vps21p (also called Ypt51p) 4 and possesses a CUE domain on the C-terminal side of the GEF domain. The CUE domain binds monoubiquitin and promotes autoubiquitination of Vps9p 5,6 . At least seven mammalian proteins contain VPS9 domains, including , the RIN family of RAS effectors 8-10 , the ALSIN protein encoded by the amyotrophic lateral sclerosis type 2 (ALS2) gene 11 , the homolog of the Caenorhabditis elegans RME-6 protein identified in a screen for receptor-mediated endocytosis 12 and the VPS9 domain-ankyrin repeat protein, VARP 13 . Despite the critical function of Rab GTPases in membrane trafficking and the obligatory requirement of GEFs for activation, little is known about the structural bases of Rab GTPase recognition and activation by Rab GEFs or the mechanisms for allosteric regulation of Rab GEF activity. To investigate the structural basis for selective activation of Rab GTPases by VPS9 domain GEFs, we determined the crystal structure of the HB-VPS9 tandem of human RABEX-5 in complex with the nucleotide-free form of human RAB21. The structure reveals how VPS9 domains recognize the GDP-bound form of RAB5-subfamil...