Molecular Architecture of the Ankyrin SOCS Box Family of Cul5-Dependent E3 Ubiquitin Ligases

Multi-subunit Cullin–RING E3 ligases often use repeat domain proteins as substrate-specific adaptors. Structures of these macromolecular assemblies are determined for the F-box-containing leucine-rich repeat and WD40 repeat families, but not for the suppressor of cytokine signaling (SOCS)-box-containing ankyrin repeat proteins (ASB1–18), which assemble with Elongins B and C and Cul5. We determined the crystal structures of the ternary complex of ASB9–Elongin B/C as well as the interacting N-terminal domain of Cul5 and used structural comparisons to establish a model for the complete Cul5-based E3 ligase. The structures reveal a distinct architecture of the ASB9 complex that positions the ankyrin domain coaxial to the SOCS box–Elongin B/C complex and perpendicular to other repeat protein complexes. This alternative architecture appears favorable to present the ankyrin domain substrate-binding site to the E2-ubiquitin, while also providing spacing suitable for bulky ASB9 substrates, such as the creatine kinases. The presented Cul5 structure also differs from previous models and deviates from other Cullins via a rigid-body rotation between Cullin repeats. This work highlights the adaptability of repeat domain proteins as scaffolds in substrate recognition and lays the foundation for future structure–function studies of this important E3 family. [Display omitted] •Crystal structures were solved for the ASB9–Elongin B/C complex and the interacting Cul5 domain.•A model for their assembly into a Cullin–RING E3 ligase was constructed.•The molecular architecture of these ankyrin-containing SOCS box proteins deviates from the related F-box proteins to maintain the precise geometry for substrate ubiquitylation.