New structural features of the APC/C revealed by high resolution cryo-EM structures of apo-APC/C and the APC/C^CDH1:EMI1complex

Abstract The multi-subunit anaphase-promoting complex/cyclosome (APC/C) is a master regulator of cell division. It controls progression through the cell cycle by timely marking mitotic cyclins and other cell cycle regulatory proteins for degradation via the ubiquitin-proteasome pathway. The APC/C itself is regulated by the sequential action of its coactivator subunits CDC20 and CDH1, post-translational modifications, and its inhibitory binding partners EMI1 and the mitotic checkpoint complex (MCC). In this study, we took advantage of the latest developments in cryo-electron microscopy (cryo-EM) to determine the structures of human APC/C CDH1:EMI1 and apo-APC/C at 2.9 Å and 3.2 Å, respectively, providing novel insights into the regulation of APC/C activity. The high resolution maps allowed the unambigious assignment of a previously unassigned α-helix to the N-terminus of CDH1 (CDH1 α1 ) in the APC/C CDH1:EMI1 ternary complex. CDH1 α1 binds at the APC1:APC8 interface, thereby interacting with a loop segment of APC1 through electrostatic interactions only provided by CDH1 but not CDC20. We also indentified a novel zinc-binding module in APC2, and confirmed the presence of zinc ions experimentally. Finally, due to the higher resolution and well defined density of these maps we were able to build, aided by AlphaFold predictions, several intrinsically disordered regions in different APC/C subunits that play a fundamental role in proper complex assembly.