Cryo-EM reveals alternative modes of dimerization driving activation of IKK

The inhibitor of κB kinase (IKK) complex integrates diverse cellular inflammatory responses, and induces transcription factor NF-κB. The molecular mechanism by which IKK becomes catalytically active in response to signaling remains unclear despite structural knowledge of the individual IKK1/α, IKK2/β, and NEMO/IKKγ protein components within its hetero-oligomeric assembly. Cryo-EM of the IKK2/β homodimer bound to an associating NEMO/IKKγ protein fragment, reveals multiple conformers. Mutual exclusivity of dimeric conformers, canonical versus alternate, is reflected in and dependent upon order-to-disorder transition of the canonical 6-helical bundle dimerization interface. Correlation of this unusual structural plasticity of IKK2/β with its biochemical and cellular activities suggests mechanistic possibilities for how association with its partner scaffold protein NEMO/IKKγ and polyubiquitin chains might dictate catalytic activation of IKK through distinct IKK2/β conformers.

The inhibitor of κB kinase (IKK) complex is central to inflammatory signaling via the NF-κB family transcription factors. Its activation mechanism has remained unclear. Cryo-EM analysis reveals that the constituent kinase IKK2/β adopts structurally distinct, mutually exclusive dimeric conformations controlled by an ordered-to-disordered transition at its canonical dimerization interface. Stabilization of select IKK2/β conformers by the scaffold protein NEMO in association with poly-ubiquitin chains is regulated through modular architecture and structural plasticity of distinctive kinase-associated domains, present only in kinases of this family. This unique regulatory mechanism governing catalytic activation of IKK2/β provides a conceptual framework for targeting dysregulated NF-κB signaling in human diseases.