Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites

The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF activity within the replication terminus macrodomain is suppressed by the sequence-specific unloader MatP. Here, we present the complete atomic structure of MukBEF in complex with MatP and DNA as determined by electron cryomicroscopy (cryo-EM). The complex binds two distinct DNA double helices corresponding to the arms of a plectonemic loop. MatP-bound DNA threads through the MukBEF ring, while the second DNA is clamped by the kleisin MukF, MukE, and the MukB ATPase heads. Combinatorial cysteine cross-linking confirms this topology of DNA loop entrapment in vivo. Our findings illuminate how a class of near-ubiquitous DNA organizers with important roles in genome maintenance interacts with the bacterial chromosome. [Display omitted] •Complete atomic structures of the bacterial SMC complex MukBEF on and off DNA•MukBEF entraps two DNA double helices when bound to the unloader MatP•In vivo topology of DNA loop entrapment determined by cysteine cross-linking•Arms of the DNA loop thread through separate compartments of MukBEF The SMC complex MukBEF organizes bacterial chromosomes into large DNA loops. In this article, Bürmann et al. report the cryo-EM structure of MukBEF bound to its unloading factor, MatP, and two DNA segments corresponding to the arms of a loop. The article provides insights into how SMC complexes topologically entrap DNA and unload from chromosomes.