(342ao) Integrative Modeling of the Smc-5/6 Protein Complex

Structural Maintenance of Chromosomes (SMC) complexes are important chromatin modulators. The Smc5/6 complex is directly involved in the regulation and repair of DNA in eukaryotes. Despite overarching topological similarities with other members of the Smc family like cohesin and condensin, Smc5/6 has distinct functions whose molecular bases remain poorly elucidated. Here, we develop an integrative model of the budding yeast Smc5/6 in complex with the SUMO ligase Nse2, and the Nse5 and Nse6 proteins. Specifically, we use crystal structures of Nse2 available from the PDB, our cryo-electron-microscopy derived 3 â„« resolution structure of the Nse5/6 subcomplex, comparative models of the globular head and hinge regions of Smc5/6 and molecular mechanics models of their coiled-coil arm regions. A multiscale model representation consisting of the aforementioned structurally covered components as rigid bodies, and all other regions as (coarse-grained) flexible beads is scored using spatial restraints designed from our dataset of ~337 unique inter-residue chemical crosslinks, in addition to fundamental physical interactions like chain connectivity and excluded volume. Structural degrees of freedom of alternate models that satisfy the input information are sampled, and a representative ensemble of good scoring models are filtered out to describe the pentamer at a precision of 30 â„«. The integrative model qualitatively and quantitatively corroborates the shape of the Smc5/6 arm region from negative staining 2D electron microscopy class averages, which were not used as input data for modeling. Unlike several examples of other SMC structures in the past literature, as well as contemporary structural investigations of the Smc5/6 complex, we provide a rigorous 3D model of the coiled-coil arm region that is structurally consistent with the input data. We find that in contrast to cohesin and condensin, the Smc5/6 arms do not fold back onto themselves; rather they interact uniquely with the Nse-s 2, 5 and 6, such that the Nse5/6 subcomplex organizes spatially as a linchpin that connects distal parts of the pentameric holocomplex.