(A) Representative simulated annealing composite omit map of the Rabex-5Δ-Rabaptin-5C212 complex. The map is contoured at 1.0σ with the final structure shown in stick model. (B) Superposition of the Rabex-5 GEF domain alone (pink, PDB code 1TXU) (Delprato et al., 2004), in the Rabex-5 GEF-Rab21 complex (green, PDB code 2OT3) (Delprato and Lambright, 2007), in the Rabex-5Δ-Rabaptin-5C212 complex (blue), and in the Rab5-Rabex-5Δ-Rabaptin-5C212 complex (cyan). The overall structure of the GEF domain in these structures is very similar with RMSD of ∼0.90 Å for 228 Cα atoms. Only slight conformational differences are observed in the αV1-αV2, αV3-αV4, and αV5-αV6 loops which are involved in the substrate binding. The regions with similar conformations are colored in gray and the regions with slightly varied conformations are marked in different colors. The invariant “aspartic acid finger” Asp313 in the αV3- αV4 loop is shown with side chain. (C) Superposition of the Rabex-5Δ-Rabaptin-5C212 complex and the Rabex-5 GEF-Rab21 complex. For the Rabex-5Δ-Rabaptin-5C212 complex, the GEF and CC domains of Rabex-5 are colored in blue and violet, respectively, and Rabaptin-5C212 in pink. For the Rabex-5 GEF-Rab21 complex, the Rabex-5 GEF domain is colored in light blue; switch I, interswitch, and switch II of Rab21 are colored in red, green and dark yellow, respectively, and the rest region in gray. The substrate-binding site of Rabex-5 in the Rabex-5Δ-Rabaptin-5C212 complex is partially occupied by the three-helix bundle formed by Rabex-5CC and Rabaptin-5C212.