We have used cryo-electron microscopy and image analysis to obtain the three-dimensional (3D) structure of 11, 12, 14 and 15 protofilament microtubules decorated with the motor domain of ncd. To obtain the 3D maps, we developed a back-projection method that does not require a helical arrangement of the tubulin heterodimers. This method allows the calculation of 3D maps even when lattice discontinuities (seams) are present. The maps show that the microtubules we studied conform to a B-type lattice with one or more seams. In the presence of 5'-adenylim-idodiphosphate (AMP-PNP), the motor domain of ncd binds to the microtubule protofilament crest interacting with only one protofilament. Viewing the structures along the microtubule axis shows that the ncd motor domain and the tubulin are titled in opposite directions. We determined that a clockwise tilt of the tubulin subunits corresponds to a view from the minus end towards the plus end of the microtubule.