Structural basis of nucleosome deubiquitination by the bidentate Calypso/ASX complex

Here we report the cryo-EM structure of Drosophila Calypso/ASX complex bound to a nucleosome, revealing the molecular basis of its chromatin interaction. Unexpectedly, only one Calypso/ASX copy engages the nucleosomal substrate in a conformation analogous to that observed in human BAP1/ASXL1, while the second unit remains structurally disengaged. We further identify the C-terminal tail of Calypso as the principal determinant of substrate affinity through direct interaction with nucleosomal DNA. Together, these findings support a model in which the bidentate Calypso/ASX complex enables processive deubiquitination along chromatin through alternating or cooperative catalytic engagement.