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Figure S4. Pseudo-atomic model for rotation of the catalytic core. The helices and ß sheets of KIF1A structures (Kikkawa et al., 2001) are shown in brown and dark green, respectively; whereas the helices and ß sheets of the ß tubulin dimer structure (Nogales et al., 1998) are shown in blue and dark green, respectively. Tubulin helices H11 and H12 (orange for ß and yellow for ) are on the outer microtubule surface forming a major part of the binding site for the Unc104 catalytic core. (A) Front and (B) side views of the KIF1A-AMPPCP structure docked into the EM map of Unc104₃₆₂-AMPPNP decorated microtubules (red wire frame). The KIF1A neck linker (red strand) is docked into the catalytic core; a dotted arrow denotes missing residues of the neck linker in the structure. The protofilament axis is vertical. (B) Side view shows that KIF1A-4 helix (red) lies centrally within the microtubule-binding interface, and lies at the COOH-terminal end of H12 in ßtubulin (orange). The 4 helix ends with the K-loop, an Unc104/KIF1 class specific insert, which is very close to the negatively charged ß tubulin COOH terminus (Kikkawa et al., 2001). (C) Front and (D) side views of the KIF1A-ADP structure docked into the EM map of Unc104₃₆₂-ADP (blue wire frame). The KIF1A 4 helix (green) is rotated away from the microtubule surface plane compared with B. (E) Front and (F) side views of the superposition of the docked X-ray structures shown in A-D. (E) Front view shows that the catalytic core in ADP (red) is slightly rotated off the protofilament axis compared with that in AMPPNP (red). The rotation is most primarily obvious at the "tip-head" of the catalytic core. We observe very small changes in the lower end of the catalytic core. (F) The side view suggest that a4 in the ADP state (green) is slightly rotated away from the microtubule surface compared with the 4 in the AMPPNP state (red).