Fig. 2: Structural variability of the mobile domain D5.

a Cryo-EM density maps of Polθ-hel in the apo form, AMP–PNP-bound form, MH search state, and MH annealed states 1 and 2. The subdomain D5 (highlighted in blue) is bound to the helicase ring at the D2–D4 interface in the apo and AMP–PNP-bound forms but becomes invisible in the MH search state. In the MH annealed states, the D5 reemerges at the dimer interface in either one protomer (state 1) or both protomers (state 2). b Superimposition of a protomer from the apo form with the MH annealed state, highlighting the displacement of D5. The C-terminal end of the C-terminal helix is marked with an asterisk. c Positioning of the relocated D5 in the dimer context, depicted in a cylinder model (blue) against the rest of the Polθ-hel dimer shown in the surface representation (grey). An overlay of the cryo-EM density over the atomic model of the relocated D5 is shown on the right. d Structure around the acidic patch of the U-shape structure in D5. Basic residues R637 and K640 of D4 in the other protomer electrostatically engage with the acidic patch. e Structure around F839 of the U-shape structure in D5. The F839 is bound at the hydrophobic cavity formed by L614, F632, L769, and W771 of D4 in the other protomer. f Proposed model of the mobile D5 during the MMEJ.