Cryo-EM density map and atomic model of nucleotide-free kinesin on the microtubule. (A–C) Cryo-EM reconstructed map of the nucleotide-free kinesin–microtubule complex (light yellow) and its refined atomic model (kinesin, pink; tubulin, gray) are shown in cartoon representation (A and B) and stick representation (C). The cryo-EM map of α4 and α6 helices is highlighted in green and orange, respectively. B and C provide close-up views of α4 and α6. (D and E) Atomic model derived from the cryo-EM map was aligned with the previously solved nucleotide-free structure of human kinesin-1 motor domain bound to tubulin–DARPin complex (green; #4LNU [Cao et al., 2014]). These structures were similar except that the N terminus of α4 of 4LNU deviated from the cryo-EM density map, as shown by the arrowhead in E. (F–H) Close-up views of the cryo-EM map and its atomic model of the kinesin–microtubule interface. The interface of kinesin with β-tubulin (F) and α-tubulin (G and H) is shown. Hydrogen bonds and salt bridges are marked as blue dashed lines.