Fig. 3: Interaction of the processive Pol δ holoenzyme with DNA.

Map region around dsDNA and model, showing that DNA is held in place by the polymerase thumb domain, and stabilized by the PCNA central channel. The N-terminal, palm and fingers domains of Pol δ and the PCNA monomer in the foreground are removed for clarity. Inset 1: Cryo-EM map region and model of primer/template DNA in the Pol δ active site. The terminal adenine in the primer strand and paired incoming dTTP are labeled. Inset 2: PCNA interactions with DNA. PCNA subunits are shown as cartoons and colored in different shades of blue. DNA is shown as a yellow ribbon. DNA phosphates within a coulombic interaction distance (<6 Å) from PCNA residues are shown as spheres. Interacting phosphates on the template and primer strands are shown in red and yellow, respectively. Phosphates closer than 5 Å are shown with a larger sphere diameter. PCNA interacting residues are shown as sticks and labeled. The asterisk indicates that the side chain of R149 is flexible, but could approach a phosphate group at a distance <6 Å.