Fig. 2: AlphaFold prediction of the Lig1–PCNA complex.
From: Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing
a First ranked model showing the Lig1 N-terminal region (residues 1-263) and Lig1 Core (residues 264-919) as yellow and red ribbons, respectively, and PCNA trimer as ribbons in different shades of blue. The insets show close-ups of the three predicted binding sites and associated aligned error (PAE), with Lig1 residues shown as sticks and PCNA as surface. The middle panel shows an overlay of the predicted PIPDBD interface (red sticks) and that from the cryo-EM structure (green sticks). The high PAE, lack of conservation and absence of experimental evidence of binding for PIP3 suggest that PIP3 is a spurious prediction. b Overlay of the AlphaFold model and cryo-EM structure on PCNA. The positions of the Lig1 Core are related by a 29° rotation around the indicated axis. The N-terminal region of the AlphaFold model and DNA in the cryo-EM model are omitted for clarity.
