Fig. 2: Cryo-EM 3D structure and dynamics of mononucleosome.
a, Cryo-EM images, and, b, nine representative particles of mononucleosome in 5 mM Na+. c, Zoomed-in images of two representative particles. Two DNA gyres and the NCP low-density central hole are indicated by orange and yellow arrows, respectively. d, 3D reconstruction process of an individual nucleosome particle, showing by raw image (ground-truth), the mask-free projection of the initial 3D map and the masked projection and final 3D map (column 1 through 4, respectively) at three representative tilting angles. In this experiment, 4 cryo-EM grids were prepared, 10 cryo-ET data sets were acquired, and all isolated particles (47 particles) were targeted for 3D reconstructions as showed in the supplementary Fig. 14-60. e,f, Perpendicular views of the final 3D map displayed by after (gray) and before (cyan) 45 Å Gaussian lowpass filtering, which superimposed with the flexibly fitted model. g, Schematic showing the angles. The orientation of the linker DNA relative to the NCP is defined as the wrapping angle α and the bending angle β, for both entry (cyan) and exit (yellow) side of the NCP. The convention of defining the negative direction as bending away from the NCP is applicable to αen, αex, βen, βex,\(\,{\theta }_{F}\), and \({\theta }_{s}\). h–j, Zoomed-in view of the NCP regions of three mononucleosomes, shown with the projection, the final map, and the fitted model, respectively. DNA on the histone is highlighted by yellow arrows. In this experiment, a total of 47 particles were reconstructed as shown in supplementary Fig. 3d-f and 14-60. for statistics. k, 30 representative density maps, shown with fitted models. l, Super-imposed 47 models aligned based on NCP portion. Models color-encoded by the \(\theta\) angle. m, Histogram of DNA-histone contact positioning. n, Histograms of DNA entry and exit positions to/from NCP. The positive values represent the events of unwrapping against the standard model. o,p, Histograms of the \(\theta\) angle and its two planar projections \({\theta }_{F}\) and \({\theta }_{S}\). q, Scatter plot and correlation between the entry and exit DNA arms. r, Scatter plot and correlation between the wrapping angle α and bending angle β. s, Superimposed vectors of both entry (yellow) and exit (green) DNA linkers on NCP (magenta). t, Histogram of the wrapping angle α and the bending angle β distribution measured from all DNA linkers.
