Alphafold 3-guided insights into the Importinβ: Importin7 heterodimer interaction and its binding to histone H1

The nuclear import of H1 linker histones is facilitated by a heterodimer of the transport receptors Importinβ (Impβ) and Importin7 (Imp7). The interaction between them is mediated by a stretch of C-terminal residues of Imp7 essential also for Imp7 activation by Impβ. An Impβ:Imp7:H1 complex model was predicted by Alphafold3 and validated using cross-linking data, isothermal titration calorimetry, and pull-down experiments, providing robust support for its accuracy. This model positions the H1 globular domain within the central cavity of Imp7. Refinement of this atomic model against a published cryo-electron microscopy (cryo-EM) map demonstrated significantly improved correspondence compared to the earlier interpretation, which placed the H1 globular domain within Impβ. This enhanced structural consistency further substantiates the accuracy of the AI-driven prediction. Moreover, a detailed analysis confirmed the extended C-terminal stretch of Imp7 harboring a nucleoporin-like binding (NlB) region with two FXFG-like nucleoporin motifs interacting with the outer surface of Impβ.