Structure and interactions of the endogenous human commander complex

The recently discovered multiprotein Commander complex is a master regulator of cellular homeostasis within endosomal transport and the trans-Golgi network. The Commander complex has been linked to the regulation of several cellular functions, including ion and lipid homeostasis, embryogenesis, immune response, cell growth, and cell cycle. It consists of ten homologous Copper-metabolism Murr1 Domain proteins (COMMD1–10), coiled-coil domain-containing proteins CCDC22 and CCDC93, vacuolar protein sorting-associated proteins VPS26C, VPS35L, and VPS29, and a DENN (differentially expressed in normal and neoplastic cells) domain-containing protein 10 (DENND10). COMMD proteins 1–10 are highly conserved sequence homologs of COMMD1 found in mammals and some in lower metazoans. COMMD1 was named after its initially discovered function in copper homeostasis regulation. Knockouts of individual COMMD proteins cause severe reduction in protein levels of all COMMD proteins, suggesting that they assemble into a larger complex. Knockdowns of COMMD proteins have been associated with developmental disorders in lower vertebrates, while in humans, missense mutations in the COMMD genes have been linked to various human diseases such as Wilson"s disease, Parkinson"s disease, atherosclerosis, as well as viral protein recycling and cancer. Despite several studies focusing on individual Commander subunits, further systematic studies that assess the complete complex are necessary to understand how the multitude of its different functions are regulated. Similarly, the structure of the Commander complex, essential for understanding its molecular function, has remained elusive. In this study, we address these critical gaps in our knowledge of the Commander complex. We report the structure of the endogenous human Commander complex determined by cryogenic electron microscopy (cryo-EM) and comprehensively map the molecular context and interactions of the Commander and individual complex interactions in human cells using affinity purification mass spectrometry (AP-MS) and proximity labelling (BioID). These findings provide a structure-based blueprint for understanding the function of the Commander complex in endosomal sorting and other essential cellular processes.