Highlights d ATG4s promote phagophore growth independently of their protease activity and ATG8s d ATG4s and their proximal partners including LRBA regulate ATG9A vesicle trafficking d AI-directed 3D EM reveals that ATG4s promote phagophore-ER contacts during mitophagy d ATG4s are not crucial for ATG8 removal from autolysosomes but can regulate ATG8ylation
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