Structures of ZYG11B-EloB-EloC-substrate complex reveal mechanisms of CRL2ZYG11B assembly and function

Abstract ZYG11B is a substrate receptor of the Cullin2-RING E3 ligase (CRL2), mediating the Gly/N-degron pathway and contributing to diverse processes including cell cycle control, protein homeostasis, apoptosis, and innate immunity. While previous studies resolved the structure of its truncated ARM domain, how full-length ZYG11B coordinates substrate engagement and CRL2 ZYG11B assembly remains unclear. Here, we present cryo-EM structures of full-length human ZYG11B in complex with the EloB–EloC adaptor and a Gly/N-degron peptide, revealing a seahorse-like architecture with distinct interfaces for adaptor and substrate binding. Unexpectedly, ZYG11B adopts both monomeric and dimeric assemblies, with the dimer stabilizing two substrate-binding sites in opposite orientations. Functional assays demonstrate that interfaces mediating adaptor recruitment, substrate binding, and dimerization are essential for substrate degradation, suggesting a dynamic mechanism involving both assembly states. These findings provide a structural framework for understanding CRL2 ZYG11B -mediated ubiquitination and offer mechanistic insights that may inform the rational design of ZYG11B-based applications.