Supplementary Figure 8: Signal subtraction and 3D classification of PRC2–Nclmod
From: Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes
(a) To better resolve the interface between PRC2 and Nclmod, Nclsub and linker DNA signal was subtracted from the raw particle images23 and alignment-free 3D classification was performed, yielding classes of varying Nclmod orientations relative to PRC2. For closer assessment of the contacts between the nucleosome and PRC2, classes 1 and 3 were chosen, since these classes showed reasonable density in the region of interest and are examples of distinct Nclmod orientations. (b) Back views of the EED-Nclmod interface comparing classes 1 (left) and 3 (right) as described in Fig. 4. Asterisks according to Fig. 4 c. Bottom panel, same view as top panel, but displayed at lower threshold. For class1, a continuous density connects the peptide density at the EED WD40 domain and the exit site of the H3 tail from Nclmod (c) PRC2-Nclmod contacts mediated by the SBD and SANT1 domains of EZH2 vary with nucleosome orientation. Dots indicate possible contacts of SANT1 with either EED or DNA. Red: possible SANT1-EED contact; green: SANT1-SRM linker density; purple: putative contact between SANT1 and the nucleosomal DNA.
