Fig. 3: The E. coli clamp loader complex (CLC) opens β₂ by crab claw-like motions.

a Cryo-EM map of CLC bound to an open clamp (CLC•β₂^open) coloured as in Fig. 2, and with the highest confidence regions of ψ(χ) in orange red. Density next to Domain I of δ’, presumed to be from the unstructured C-terminal region of a γ/τ subunit is coloured white and indicated by a red asterisk. Top right, close-up view showing the unassigned EM density near the N-terminus of δ’. A moving window of 8-residue peptides selected from the C-terminal flexible region of γ were docked into δ’ and scored against the density. The best scoring peptide corresponded to the moderately-conserved γ residues Val403−Thr409. This assignment is yet to be verified experimentally. Bottom right, unsharpened EM density of the CLC-binding peptide of ψ (Thr2–Glu28) that bridges all three γ subunits³⁰. b Interface areas between AAA+ modules increase significantly in the transition from CLC•β₂^closed to CLC•β₂^open. Source data are provided as a Source Data file. c Conformational changes of the AAA+ modules during transition from CLC•β₂^closed to CLC•β₂^open. While the AAA+ modules of γ2, γ3 and δ’ barely move, those of γ1 and δ swing outwards, resulting in expansion of the CLC and opening of β₂. Structures were superimposed by aligning the γ2 subunit using MatchMaker in Chimera⁷⁶. Arrows indicate movements of individual subunits. d Orthogonal views of conformational changes in β₂ during transition from CLC•β₂^closed to CLC•β₂^open. The clamp remains mostly flat after opening. Most obvious motions are on the β-I subunit with Domain I rotating around Domain III of β-II and Domains II–III around Domain I. e Conformational changes in the final stage of clamp opening revealed by 3D variability analysis. The resolution at which eigenvectors of 3DVA are filtered was set to 5 Å. Volumes of the first and last frames of principal component_000 of 3DVA that illustrate the most significant and biologically relevant conformational changes are presented.