Figure 4.

Nucleotide-Driven Structural Changes

(A–C) Three views showing changes in density between dynein-c heads prepared in the absence of nucleotide and with ADP.Vi bound. Maps were filtered to the same resolution (22 Å), normalized to a mean voxel intensity of 0 and σ of 1, aligned, and subtracted pairwise from each other. Voxel intensities in the resulting difference maps were used to color the surface of each map, according to the chart. Maroon indicates a positive change in density from the other structure, whereas cyan indicates a negative change. Insets show corresponding views of S. cerevisiae cytoplasmic dynein crystal structure colored as in Figure 1. Changes at the linker contact site (B, arrows) and between AAA1 and AAA2 (C, arrowheads) are indicated.

(D) Enlargement showing the D. discoideum dynein crystal structure (PDB 3VKG) (Kon et al., 2012) docked into the ADP.Vi-dynein-c map (wire mesh). Interacting residues between the linker and the β hairpin inserts in AAA2 in the crystal structure are shown (yellow sticks). The single α helix spanning the cleft in the linker is indicated with an arrow.