Alphafold 3 guided insights into the Importin b / Importin 7 heterodimer interaction and its binding to Histone H1

Abstract

The nuclear import of H1 linker histones is facilitated by a heterodimer of the transport receptors Importin{beta} (Imp{beta}) and Importin7 (Imp7). While both importins can individually interact with H1, only their preassembled hetero-dimer enables its proper binding for translocation through the nuclear pore. The interaction between Imp7 and Imp{beta} is mediated by a short stretch of residues in the C-terminal region of Imp7, which plays a key role in Imp7 activation by Imp{beta}. This interaction is allosterically regulated by Imp{beta}, finely tuning the activity of the Imp{beta}/Imp7 heterodimer. A complete model of the Imp{beta}:Imp7:H1 complex was predicted by Alphafold3 (AF3) and subsequently validated using cross-linking (X-link) data, isothermal titration calorimetry (ITC), and pull-down experiments, providing robust support for the models accuracy. This model positions the globular domain of H1 within the central cavity of Imp7, in agreement with cross-linking data. Refinement of this atomic model against a previously published cryo-EM map demonstrated significantly improved correspondence compared to the earlier interpretation, which placed the H1 globular domain within Imp{beta}. This enhanced structural consistency further substantiates the accuracy of the AI-driven prediction. Detailed analysis identified the nucleoporin-like binding (NlB) region of Imp7 as a short stretch interacting with the outer surface of Imp{beta}. This interaction mode implies that regulation of FG-binding site accessibility on Imp{beta}, mediated by the FXFG nucleoporin motives within the Imp7 NlB region, likely modulates transport pathways and/or enhances the efficiency of H1 nuclear import.