Fig. 4: REST revealed continuous conformational changes of nucleosome linker DNA in simulated dataset (SIM5).
From: A method for restoring signals and revealing individual macromolecule states in cryo-ET, REST
A A series of dynamic nucleosomes generated by using NMA. B Examples of four training pairs. Top: the input of training pairs generated from the corresponding ground truth particle with noise (SNR 0.1) and a missing wedge (±40°) superimposed (low-quality). Bottom: the ground truth of the training pairs generated from the atomic model (high-quality). C A 3D rendering of the restored tomogram. Each nucleosome could be identified with different linker DNA conformation. D Eight representative particles from A showing the motion of linker DNA from closed state (cyan) to open state (pink) via middle transitions (gray). E Compared with the 3D density improved by Topaz-Denoise and IsoNet (left), REST could effectively clean the noise density and eliminate elongation and distortion (right). The region was from simulated tomogram of particles in A and rotated around the x-axis by 45°.
