Cryo-EM structure and dynamics of eukaryotic DNA polymerase [delta] holoenzyme

DNA polymerase [delta] (Pol[delta]) plays pivotal roles in eukaryotic DNA replication and repair. Pol[delta] is conserved from yeast to humans, and mutations in human Pol[delta] have been implicated in various cancers. Saccharomyces cerevisiae Pol[delta] consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits. Here, we present the near atomic resolution (3.2 Å) cryo-EM structure of yeast Pol[delta] holoenzyme in the act of DNA synthesis. The structure reveals an unexpected arrangement in which the regulatory subunits (Pol31 and Pol32) lie next to the exonuclease domain of Pol3 but do not engage the DNA. The Pol3 C-terminal domain contains a 4Fe-4S cluster and emerges as the keystone of Pol[delta] assembly. We also show that the catalytic and regulatory subunits rotate relative to each other and that this is an intrinsic feature of the Pol[delta] architecture. Collectively, the structure provides a framework for understanding DNA transactions at the replication fork.