Structural basis of condensin II activation

Abstract Condensin II is present in the nucleus throughout interphase, yet does not acquire robust loop-extruding activity until cells enter prophase. How the complex is kept inactive before prophase has remained unclear. Here we show, by cryo-EM and mass photometry, that nucleotide-free human condensin II forms a reversible dimer at physiological ionic strength. In this dimer, CAP-H2 elements required for chromosome association are buried, while the C-terminal tail of CAP-D3 holds the neck gate open by blocking engagement of the CAP-H2 neck-binding domain with the SMC2 neck. Nucleotide binding promotes monomerization and causes the SMC module to rotate toward the displaced neck-binding domain, but persistent CAP-D3 blockade keeps the gate open. These structures explain CAP-D3-dependent self-suppression of condensin II activity and suggest how nucleotide binding and M18BP1 engagement promote progression from an autoinhibited state toward a poised, pre-clamping intermediate.