Fig. 2.

The high-affinity, MT-bound state of the dynein MTBD is characterized by repositioning of helices H1 and CC1. (A) Rigid-body docking of the low-affinity MTBD structure into our cryo-EM density. (B) Pseudo-atomic model of the high-affinity MTBD bound to MTs generated by Molecular Dynamics Flexible Fitting (MDFF) and Targeted Molecular Dynamics (TMD) (see text for details). (C) Close-up of the structure shown in (A), with its orientation indicated in panel (A). (D) Close-up of the structure shown in (B), with its orientation indicated in panel (B). The cryo-EM map is shown as a transparent grey mesh. The MTBD is colored following the scheme shown at the bottom of the figure and structural elements are indicated in the different views. H1 (orange/red) is the element with the largest movement in the transition to the high-affinity conformation; H3 and H6 (dark blue) are major contact points with the MT (green). α- and β-tubulin are indicated (green). MT polarity is indicated in panels A and B. H1 protrudes from the cryo-EM map and clashes with the MT in the rigid-body docked low-affinity state (A and C).