Architecture of the mycobacterial type VII secretion system

Host infection by pathogenic mycobacteria such as Mycobacterium tuberculosis is facilitated by virulence factors secreted by type VII secretion systems1. Here we report the cryo-electron microscopy structure of a membrane-embedded core complex of the ESX-3/type VII secretion system from Mycobacterium smegmatis at 3.7 A resolution. The core of the ESX-3 secretion machine consists of four protein components, EccB3:EccC3:EccD3:EccE3 in a 1:1:2:1 stoichiometry, building two identical protomers. The EccC3 coupling protein comprises a flexible array of four ATPase domains, which are linked to the membrane through a stalk domain. The ‘domain of unknown function’ (DUF) adjacent to the stalk is identified as an ATPase domain essential for secretion. EccB3 is predominantly periplasmatic but a small segment crosses the membrane and contacts the stalk domain, suggesting that conformational changes in the stalk domain triggered by substrate binding at the distal end of EccC3 and subsequent ATP hydrolysis in the DUF could be coupled to substrate secretion to the periplasm. Our results reveal that the architecture of type VII secretion systems differs markedly from other known secretion machines2.