Extended Data Fig. 4: Cryo-EM data collection and structure determination of DNMT3A2-3L oligomer complex.
From: Mechanisms of DNMT3A–3L-mediated de novo DNA methylation on chromatin
a, The UV (280 nm) absorption profile of cross-linked DNMT3A2-3L-NCP sample collected from bottom to top (left). Native gel analysis of cross-linked DNMT3A2-3L oligomer complex (right). For gel source data, see source data file. b, Representative micrograph of DNMT3A2-3L complex with one particle highlighted in green circle of 300 Å diameter. c, Representative 2D class-averages. d, Workflow of cryo-EM data processing and 3D reconstructions in CryoSPARC (4.6.0). Boxed 3D classes were selected for further processing. The final global nominal resolution for the DNMT3A2-3L oligomer complexes was 3.66 Å for the dodecamer and 3.62 Å for the octamer. e, Color-coded local resolution maps for DNMT3A2-3L dodecamer in two different orientations and overall atomic model fitting into the cryo-EM map density. Inlet, overlay of distal EM density with DNMT3L (pink) at lower contour, which was omitted from the final model, indicating the dodecamer. Half-map cFSC plots and angular distribution plots obtained from CryoSPARC were shown at the bottom. f, Color-coded local resolution maps for DNMT3A2-3L octamer in two different orientations and overall atomic model fitting into the cryo-EM map density. Inlet, overlay of distal EM density with DNMT3L (pink) at lower contour, which was omitted from the final model, indicating further oligomerization. Half-map corrected cFSC plots and angular distribution plots obtained from CryoSPARC were shown on the right.
