Fig. 1: Cryo-EM structure of the Lig1–DNA–PCNA complex.
From: Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing
a Disorder prediction against residue number of human Lig1, and Lig1 domain organization and position of PIPN-term and PIPDBD; Disorder prediction was performed with PrDOS70. The red dotted line corresponds to a disorder tendency of 0.5. The black line corresponds to Lig1 residues visible in the cryo-EM reconstruction. b Sequence alignment of ligases at the PIPN-term and PIPDBD regions. Residues of the canonical PIPN-term are shaded in gray, C-terminal basic residues are colored in blue. Residues in α-helical conformation at the N-terminus of PIPDBD in human Lig1 and ssLig18 cryo-EM structures are shaded in blue. c Two views of the cryo-EM density map of the Lig1−DNA−PCNA complex colored by domains. The sequence of the nicked DNA substrate used in the study is shown. The region shaded in gray corresponds to the nucleotides modeled in the structure. The red arrow indicates the position of the nick. d Side view of the model of the Lig1−DNA−PCNA complex shown in ribbon representation and colored by domains. The insets show cryo-EM map regions around different model elements depicted as sticks. The dotted line in the DNA substrate inset indicates the DNA helical axis. e Details of the model at the Lig1−PCNA binding site. Lig1 residues are shown as sticks, and PCNA as surface. f Motion represented by the first eigenvector from multi-body analysis. The first vector represents a motion involving a ~23° rotation of the Lig1−DNA body around an axis encompassing the DBD longitudinally. Five positions of the Lig1−DNA body spanning the full motion are shown. This mobility indicates that the Lig1 loop interacting with PCNA is malleable to support flexible tethering of the ligase to PCNA.
