Fig. 3: Cryo-EM reconstructions of MT-bound Pbkinesin-8B-MD.

a Asymmetric unit of GMPCPP-MT-bound NN Pbkinesin-8B-MD as solid surface towards NBS (threshold = 0.0322). Pbkinesin-8B-MD-NN is dark green, α/β-tubulin dark/light grey, respectively; region around NBS depicted in b is boxed. b Zoom-in of NN Pbkinesin-8B-MD NBS with docked model, showing contact formed between the helical turn (arrow) in loop 11 (yellow) and α-tubulin, P-loop (orange) in the empty NBS, and density corresponding to flexible-appearing loop 9 (blue). Pbkinesin-8B-MD-NN model is dark green, α/β-tubulin dark/light grey, respectively. c MT-bound NN Pbkinesin-8B-MD as solid surface towards the neck linker region (threshold = 0.0322). Pbkinesin-8B-MD-NN is dark green, α/β-tubulin are dark/light grey respectively; region around the neck linker depicted in d is boxed. d Zoom-in of NN Pbkinesin-8B-MD neck linker region with docked model, showing density corresponding to loop 12 (fuchsia) at C-terminus of helix-α4 that contacts β-tubulin, adjacent to which is density corresponding to the N-terminal end of the neck linker (red), which is directed towards the MT minus end. e Asymmetric unit of GMPCPP-MT-bound AMPPNP Pbkinesin-8B-MD as solid surface towards NBS (threshold = 0.0249). Pbkinesin-8B-MD-AMPPNP is light green, α/β-tubulin dark/light grey respectively; region around NBS depicted in f is boxed. f Zoom-in of AMPPNP Pbkinesin-8B-MD NBS with docked model, showing weaker loop 11 density (dashed yellow line), the P-loop (orange) adjacent to density corresponding to AMPPNP in NBS and density corresponding to flexible-appearing loop 9 (dashed blue line). AMPPNP Pbkinesin-8B-MD model is light green, α/β-tubulin dark/light grey, respectively. g MT-bound AMPPNP Pbkinesin-8B-MD depicted as solid surface towards the neck linker region (threshold = 0.0249). Pbkinesin-8B-MD-AMPPNP is light green, α/β-tubulin are dark/light grey respectively; region around the neck linker depicted in h is boxed. h Zoom-in of AMPPNP Pbkinesin-8B-MD neck linker region with docked model, showing density corresponding to loop 12 (fuchsia) at the C-terminus of helix-α4 that contacts β-tubulin, and weaker neck linker density (red dotted line), directed towards the MT minus end. i Cα RMSD (Å) of Pbkinesin-8B-MD-NN compared to AMPPNP models aligned on helix-α4 of Pbkinesin-8B-MD, depicted on the NN model; the small range of RMSD observed illustrates that only minor structural changes are detected when AMPPNP binds.