Fig. 5: Models comparing interactions of Arp3 with the mother filaments in branch junctions with bound ADP or ADP-BeFx. See also Supplementary Movie 1.
a Low-resolution rendering of the interaction of Arp3 with the mother filament in our atomic model of the ADP branch junction. b Rendering of Arp3 on the mother filament with subdomains marked SD1-SD4 as in Fig. 4. The arrows and numbers indicate the rotations and center of mass displacements of the Arp3 outer (pale orange isosurface) and inner (orange isosurface) domains with respect to the mother filament (light gray) going from the ADP-BeFx to the ADP-state. The D-loop in SD2 of Arp3 is farther from the mother filament with bound ADP than ADP-BeFx owing to a combined 1.8° rotation (left curved arrow) and 0.5 Å translation (upper left 3D arrowhead) of the Arp3 outer domain with respect to the mother filament. Colored cylinders show the axes of inner/outer subdomain rotation with respect to the mother filament (calculated in a similar manner to Fig. 4e–g). ∆∆Θ and ∆∆T are the end-to-end bending and twisting angle differences between ADP and ADP BeFx from Fig. 2h, j. c Detail of the Arp3 SD2/D-loop region indicating contacts between SD2 and mother filament subunits M4 and M5. Unmodeled density corresponding to the Arp3 D-loop extends toward and makes contact with M5, while the globular portion of SD2 makes contact with M4. d A hydrophobic contact between SD2 and M5 loosens in the transition from ADP-BeFx to ADP branch complex structures. The alpha helix containing A228 and A231 in M5 follows the movement of SD2, but moves only 0.3 Å; Correspondingly, the distances between these residues and the Arp3 loop containing S85, A86 in increases by ~0.5 Å. Low-resolution isosurface representations (20 Å resolution) in a and b were generated by the UCSF ChimeraX ‘molmap’ command.
