Subdomain motions associated with the allosteric conformational changes of kinesin motor domain on the microtubule. (A) Residues classified into three subdomains are colored in magenta (R-domain), cyan (F-domain), and green (B-domain). (B–D) Three classes of conformational state of the kinesin motor domain (Fig. 3) bound to the microtubule, colored by subdomain. Unassigned residues, which are disordered in the semi-open state, are yellow, and the neck linker is red. The kinesin–microtubule complex models of semi-open and closed states were prepared by fitting 5LT1 and 4HNA onto the cryo-EM density maps of ADP-bound (Sindelar and Downing, 2010) and ADP·AlFx-bound (Shang et al., 2014) states, respectively. For clarity, we depicted the semi-open state with MgADP bound by incorporating the MgADP from the 1BG2 structure into the 5LT1 (nucleotide-free) structure. The rotational movements of R- and F-domains relative to the microtubule—from semi-open to open and from open to closed—are represented by angular changes in the long axes of α6 and α2 helices (arrowheads), respectively.
