Figure 3: Subdomains orientation changes along the kinesin mechanochemical cycle.
From: The structure of apo-kinesin bound to tubulin links the nucleotide cycle to movement
The angles are those of the rotations needed to superimpose the P-loop (salmon, with the P-loop in orange) and Switch I/II (blue, Switch1/L9 in darker blue) subdomains, after the tubulin-binding blocks (pink) have been superimposed. The Switch2/L11 loop is in darker pink. The root mean square deviation of Cα positions after superposition are all smaller than 1 Å. The rotation axes are schematized taking the microtubule (depicted as a cylinder, with its polarity indicated) as a reference. Note that the rotations that relate subdomains in detached kinesin and in the ATP-like complex are around nearly parallel axes so that the three subdomains were not readily identified based on these two structures. The yellow disk indicates the status of the neck linker, which docks along with ATP binding but does not in the nucleotide-free state. After phosphate release and detachment from the microtubule, kinesin–ADP undergoes recovery to a state in which the neck linker undocks and becomes disordered, as schematized.
