Supplementary Figure 2: Cryo-EM analysis and resolution of CBF3−CEN3 complex.

a, A typical cryo-EM micrograph of CBF3–CEN3 representative of 3,537 micrographs. b, Gallery of 2D class averages of CBF3−CEN3 complex showing different views representative of 100 2D classes. c, Angular distribution plot of CBF3−CEN3 particles. d, Workflow of 3D classification of CBF3−CEN3 showing a 4.4-Å map of dimeric CBF3−CEN3 complex and a 3.0-Å map of CBF3^core−Ndc10^DBD (lower right) (masked EM density). Red boxes, dimeric CBF3−CEN3; black box, CBF3^core; blue box, monomeric CBF3−CEN3 (CBF3^core and Ndc10 dimer); black box, CBF3^core. The dashed-line red box shows different DNA conformations. A HEAT map representing the structural variation of the three 3D classes of the dimeric CBF3–CEN3 complex is shown in Supplementary Fig. 4c. e, Local-resolution map of multi-body segment CBF3^core of CBF3A. f, Local-resolution map of multi-body segment CBF3^core of CBF3B. g, Local-resolution map of multi-body segment of Ndc10^DBD−CEN3−DNA. h, Cryo-EM density of the 4.4-Å CBF3−CEN3 complex (left) and local-resolution map calculated with RESMAP 56 (right). i, Fourier shell correlation (FSC) curves are shown for the cryo-EM reconstructions of CBF3–CEN3 and three multi-body segments CBF3^core-A, CBF3^core-B and Ndc10^DBD−CEN3−DNA. j, Fourier shell correlation (FSC) curves are shown for CBF3^msk (gold-standard FSC, two half maps, and merged map). The resolution at FSC = 0.5 for the model–map comparison is indicated. k, Representative EM densities of regions of the 3.0-Å map of CBF3^msk.