Fig. 4. High-resolution EM maps of Kar3 motor domains bound to microtubules. (A,C) Sections at two different levels through maps of the Kar3 motor domain in three different nucleotide states (ADP-bound, empty or AMPPNNP-bound) with the Kar3-ADP crystal structure (cyan -helices and β-strands; PDB code 1F9T) (Yun et al., 2001) docked into the EM density (represented by red and grey nets) (Hirose et al., 2006). The view is from the MT plus end and the positions of sections A and C within the 3D structure are indicated in panels B,D. Parts of - and β-tubulin are included, with the crystal structures (PDB code 1JFF) (Löwe et al., 2001) shown in gold and green. The red arrowhead in A indicates a feature in the EM density of the nucleotide-free Kar3 that is absent from either of the nucleotide-bound motors and may be loop L7 in a new position. Blue arrowheads in A indicate the point at the top of the motor domain that is retracted in the empty structure. A also shows a movement of helix 5, which is closer to tubulin in the empty and AMPPNP-bound states. A black arrowhead in C indicates a marked loss of density from the region occupied by the switch-II-helix 4 in the other structures. Orange arrowheads point to the L12 loop that also disappears in the empty structure. (E) Sections though the three maps viewed from the side. There are changes in the position of helix 6 relative to switch II helix 4 and helix H12 of -tubulin but, with only one Kar3 crystal structure available, we cannot be certain that the movement is the same as in Kif1a (Fig. 3C).