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Significance C9ORF72, together with SMCR8 and WDR41, can form a stable complex that regulates membrane trafficking. We report the cryo-EM structure of the C9ORF72–SMCR8–WDR41 complex at atomic resolution. Notably, the stoichiometry of the three subunits in the C9ORF72–SMCR8–WDR41 complex is 2:2:2. Interestingly, the C termini of C9ORF72 and the DENN domain of SMCR8 mediate the dimerization of the two C9ORF72–SMCR8–WDR41 protomers in the complex. Moreover, WDR41 binds to the DENN domain of SMCR8 by the C-terminal helix without direct contact with C9ORF72. Most importantly, the C9ORF72–SMCR8 complex works as a GAP for Rab8a and Rab11a in vitro, and the Arg147 of SMCR8 is the arginine finger.

Cryo-EM structure of C9ORF72–SMCR8–WDR41 reveals the role as a GAP for Rab8a and Rab11a