Structural basis of an endoplasmic reticulum EMC:Spf1 insertase–dislocase complex

Most eukaryotic membrane proteins are inserted into the membrane at the endoplasmic reticulum (ER). This essential process relies on molecular quality control machineries to prevent mistargeting and incorrect structure formation. Here, we show that the ER membrane protein complex (EMC) forms an evolutionarily conserved supercomplex with the P5A-ATPase Spf1/ATP13A1. Biochemical, structural and cellular analyses demonstrate that the EMC and Spf1 associate in a stoichiometric manner and retain their individual catalytic activities, the transmembrane domain (TMD) insertase function of the EMC and the TMD dislocase activity of Spf1. Our cryo-electron microscopy structures show that the EMC insertase cavity and the Spf1 dislocase cleft are positioned in close proximity within the membrane and reveal that the ATPase cycle of Spf1 remodels the interface between the two machineries and alters cytoplasmic accessibility of both substrate-binding cavities. Together, our study provides structural insights into how membrane protein insertion and extraction machineries can be spatially coordinated at the ER membrane, suggesting that functionally distinct proteostasis factors can assemble into hubs to support membrane protein biogenesis and quality control.