Raman et al. demonstrate transient SUMO-dependent complex formation between the AAA ATPase MDN1 and PELP1 during 60S biogenesis. They show that SUMO conjugation to PELP1 recruits MDN1 to pre-60S particles, while reversal of this modification by SENP3 is needed for the release of both factors during mammalian pre-ribosome remodeling.