The Commander complex is a highly conserved, multiprotein assembly that plays a vital role in endosomal recycling, a process essential for maintaining cellular homeostasis. Mutations in Commander subunits are linked to 3C/Ritscher-Schinzel (RSS) syndrome which results in abnormal skeletal, brain, kidney, and cardiovascular development. Commander is organized into two main subassemblies: Retriever, a trimer of VPS35L, VPS26C, and VPS29, and the CCC complex, which comprises coiled-coil proteins CCDC22 and CCDC93, along with ten COMMD proteins. Our recent structural studies, published in Cell (Healy et al., 2023), used an integrative structural approach to provide a detailed architectural model of the 16-subunit Commander complex (which was subsequently confirmed by two independent groups). This revealed an intricately assembled protein complex with a central heterodecameric ring comprised of the 10 COMMD proteins, this ring is then connected to the Retriever subassembly via the two CCDC proteins. Key intermolecular interactions “lock’ this complex into a compact structure.
Building upon this structural foundation, we next sought to elucidate the regulatory mechanisms governing cargo entry into the Commander recycling pathway. We investigated how Commander interfaces with sorting nexin (SNX)17, a cargo adaptor protein that selectively binds to membrane proteins destined for recycling. Using recombinant protein reconstitution and AlphaFold2 modeling, we identified a conserved mechanism by which the unstructured tail of SNX17 interacts specifically with Retriever. Our findings reveal that SNX17 typically exists in an autoinhibited state, with its C-terminus occupying the cargo binding groove. Competitive binding by endosomal cargo releases this autoinhibition, allowing the tail of SNX17 to engage with Retriever.
This SNX17-Retriever interaction is crucial for the selective handover of integrin and lipoprotein receptor cargoes into pre-existing endosomal sub-domains, preparing them for entry into the recycling pathway. Molecular cell biology and high-resolution microscopy confirmed that this interaction is a central regulatory step in Commander’s function, underscoring its importance in maintaining cellular homeostasis and supporting normal skeletal, brain, kidney, and cardiovascular development. By describing both the structure and cargo-regulation mechanism of the Commander complex, our work provides comprehensive insights into the molecular underpinnings of this critical cellular pathway.