Highlights d Smc1 and Smc3 ATPase heads adopt an engaged (E) and a juxtaposed (J) state in vivo d Smc ATPase heads delimit an Smc (S) and a kleisin (K) compartment d Single DNA molecule can be entrapped inside K compartments of either E or J type d Sister DNAs are entrapped in J-K compartments with J-head Smc3 being acetylated
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