Extended Data Figure 8: Conformational change of DNMT3A induced by histone H3 tail.

a, Average B factors for domains of ADD–CD–C^DNMT3L in the structures of ADD–CD–C^DNMT3L and ADD–CD–C^DNMT3L bound to H3 peptide. The average B factor of the ADD domain is higher than other domains in both structures, and is higher in autoinhibitory form (177.5 Å²) than that in active form (107.6 Å²). The results indicate that the ADD domain is more dynamic than other domains of the complex, especially in its autoinhibitory form. The observation further supports the idea that DNMT3A undergoes conformational changes on the ADD domain induced by histone H3. b, Two different views of the electron microscopy density maps of DNMT3A2–C^DNMT3L (left) and DNMT3A2–C^DNMT3L-H3 (right) processed to 24 Å and 20 Å resolution, respectively. The corresponding crystal structure was fitted into the electron microscopy density map for each state. The density is not fully occupied, which might because of the missing PWWP domain in the crystal structures. c, Typical negative stain CCD images of DNMT3A2–C^DNMT3L (left) and DNMT3A2–C^DNMT3L-H3 (right). Representative particles are highlighted by white boxes. d, Comparison of the two-dimensional projections (bottom) from the electron microscopy map with the corresponding reference-free two-dimensional class averages (top) reveals similar structural features. e, Position of residues F827 and F868 for ¹⁹F NMR measurements. Close-up view of the DNMT3A structure in autoinhibitory form with residues F827 and F868 indicated in stick representation. Residue F827 is located in loop L2 (for DNA binding) and close to the ADD domain. As a negative control, residue F868 is located close to the catalytic cavity and away from the ADD domain. Residue F868 is unlikely to undergo conformational change when the ADD domain dissociates from the CD domain. To detect conformational changes of DNMT3A in solution, residues F827 and F868 were substituted by ¹⁹F-labelled l-4-trifluoromethylphenylalanine (¹⁹F-tfmF) in ADD–CD. f, One-dimensional ¹⁹F NMR measurements were performed using ADD–CD with substitution of F827tfmF (left) or F868tfmF (right) in the absence or presence of H3K4me0 or H3K4me3 peptide. The chemical shift for each measurement is indicated.