Structures of APC/CCdh1 with substrates identify Cdh1 and Apc10 as the D-box co-receptor

The ubiquitylation of cell-cycle regulatory proteins by the large multimeric anaphase-promoting complex (APC/C) controls sister chromatid segregation and the exit from mitosis(1,2). Selection of APC/C targets is achieved through recognition of destruction motifs, predominantly the destruction (D)-box(3) and KEN (Lys-Glu-Asn)-box(4). Although this process is known to involve a coactivator protein (either Cdc20 or Cdh1) together with core APC/C subunits(1,2), the structural basis for substrate recognition and ubiquitylation is not understood. Here we investigate budding yeast APC/C using single-particle electron microscopy and determine a cryo-electron microscopy map of APC/C in complex with the Cdh1 co-activator protein (APC/C-Cdh1) bound to a D-box peptide at similar to 10 angstrom resolution. We find that a combined catalytic and substrate-recognition module is located within the central cavity of the APC/C assembled from Cdh1, Apc10-a core APC/C subunit previously implicated in substrate recognition(5-7)-and the cullin domain of Apc2. Cdh1 and Apc10, identified from difference maps, create a co-receptor for the D-box following repositioning of Cdh1 towards Apc10. Using NMR spectroscopy we demonstrate specific D-box-Apc10 interactions, consistent with a role for Apc10 in directly contributing towards D-box recognition by the APC/C-Cdh1 complex. Our results rationalize the contribution of both co-activator and core APC/C subunits to D-box recognition(8,9) and provide a structural framework for understanding mechanisms of substrate recognition and catalysis by the APC/C.