Importins recognize the winged-helix fold of ETS transcription factors to mediate nuclear import

Protein trafficking between the cytoplasm and the nucleus is a fundamental process in eukaryotic cell biology. While linear nuclear localization signals (NLSs) are well-characterized, many nuclear proteins lack a predictable NLS. Here, we identify the ETS domain, a DNA-binding winged-helix fold, from ETS family transcription factors as a structure-encoded NLS. We show that ETS domains mediate nuclear import through direct recognition by multiple nuclear transport receptors, including IPO9. Cryo-electron microscopy analysis of the EHF:IPO9 complex reveals that the IPO9 wraps around the ETS domain and engages structural features throughout the winged-helix fold. Biochemical studies demonstrate that the ETS domain DNA-binding helix is critical for importin recognition and for NLS activity in mammalian cells. Comparison of IPO9 bound to EHF and the histone H2A:H2B dimer reveals distinct interaction hotspots, illustrating how IPO9 employs unique combinatorial binding surfaces to accommodate structurally diverse cargos. These findings define a new class of globular NLSs and highlight the adaptability of importins in recognizing distinct protein folds. Significance Statement Nuclear import is essential for transcription factor function. However, many nuclear proteins lack recognizable nuclear localization signals (NLSs), leaving their trafficking mechanisms unresolved. Here, we identify the winged-helix DNA-binding domain of ETS transcription factors as a structure-encoded NLS shared across the ETS family of proteins. We show that multiple importins directly interact with this globular domain and define the molecular basis for cargo recognition by determining the cryo-EM structure of an importin bound to an ETS family protein. These studies establish a new class of globular NLSs and shed light on how individual importins can recognize diverse protein folds. We also provide mechanistic insight into nuclear trafficking defects that are caused by disease-linked ETS transcription factor mutations.