Supplementary Figure 12: Masked refinement after signal subtraction of PRC2–DiNcl30 and comparison with PRC2–DiNcl35 map
From: Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes
(a) Reconstruction of PRC2-DiNcl30 after subtracting the signal of Nclmod. Coloring according to the scheme in Fig. 1. (b) FSC plot indicating an improved overall resolution of 7.7 Å of the EM map after signal subtraction, according to the FSC = 0.143 gold standard criterion (Rosenthal and Henderson, J. Mol. Biol. 333, 721-745, (2003), Scheres and Chen, Nat. Methods 9, 853-854, (2012)). (c) Map of the PRC2-DiNcl30 complex after signal subtraction colored according to local resolution ranging from 8-12 Å. Right, inset showing the CXC domain as an enlarged view. Local resolution estimation determined with BLOCRES (BSOFT package (Heymann and Belnap, J. Struct. Biol. 157, 3-18, (2007)). (d) Comparison of the overall fits of the PRC2 atomic model as shown in Fig. 2 into the density map of PRC2-DiNcl35 (light yellow, map low-pass filtered to 7 Å) and PRC2-DiNcl30 (light gray). The two maps have been aligned based on their EED and EBD densities. (e) EM densities of the CXC domain of EZH2 within the PRC2-DiNcl35 (light yellow, left panels) and PRC2-DiNcl30 (light gray, right panels) complexes. The model (see methods and Supplementary Fig. 6d) was fitted into the PRC2-DiNcl35 map (low-pass filtered to 7 Å). The CXC domain deviates from the otherwise good fit of the atomic model of PRC2 in the PRC2-DiNcl30 complex. The first zinc cluster of CXC is potentially more flexible in PRC2-DiNcl30 and not as well resolved (top panel, back view). The DNA binding site of the CXC is tilted towards the back of PRC2 and the SET domain (red arrow, lower panels, bottom view).
