Structural basis for the ARF GAP activity and specificity of the C9orf72 complex

Mutation of C9ORF72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontal temporal degeneration (FTD), which is attributed to both a gain and loss of function. C9orf72 forms a complex with SMCR8 and WDR41, which was reported to have GTPase activating protein activity toward ARF proteins, RAB8A, and RAB11A. We determined the cryo-EM structure of ARF1-GDP-BeF3- bound to C9orf72:SMCR8:WDR41. The SMCR8(longin) and C9orf72(longin) domains form the binding pocket for ARF1. One face of the C9orf72(longin) domain holds ARF1 in place, while the SMCR8(longin) positions the catalytic finger Arg147 in the ARF1 active site. Mutations in interfacial residues of ARF1 and C9orf72 reduced or eliminated GAP activity. RAB8A GAP required similar to 10-fold higher concentrations of the C9orf72 complex than for ARF1. These data support a specific function for the C9orf72 complex as an ARF GAP. The structure also provides a model for the active forms of the longin domain GAPs of FLCN and NPRL2 that regulate the Rag GTPases of the mTORC1 pathway. C9orf72:SMCR8:WDR41 complex has been reported to have GAP activity for both ARF family proteins and the RAB proteins RAB8A and RAB11A. Here the authors provide structural and biochemical evidence for a specific function of the C9orf72 complex as an ARF GAP, and a structural framework for the GAP activity of the longin-containing GAP family.

Automated summary

Mutation of C9ORF72 is a common genetic cause of ALS and FTD, leading to both gain and loss of function. The C9orf72 complex with SMCR8 and WDR41 has GAP activity for ARF family proteins and RAB proteins. The study provides evidence for the specific function of the C9orf72 complex as an ARF GAP and a structural framework for the longin-containing GAP family.