Extended Data Figure 7: Structure of ADD–CD–C^DNMT3L-H3 in active form.

a, Ribbon representations of the overall structures of the ADD–CD–C^DNMT3L in active (left) and autoinhibitory (right) forms. Histone H3 peptides are coloured in yellow. b, Structural comparison of human ADD–CD–C^DNMT3L–H3 and mouse CD^Dnmt3a–C^Dnmt3L complexes. The compared structures are shown in ribbon representations. The ADD–CD–C^DNMT3L complex structure (this study) is coloured as in Fig. 1d, and the CD^Dnmt3a-C^Dnmt3L complex structure²² is coloured in grey. Residues 611–620 and 833–846 of DNMT3A were not built in the model because they lacked electron density. c, LIGPLOT representation of the ADD–CD interactions in the ADD–CD–C^DNMT3L-H3 structure. Carbon, oxygen, and nitrogen are shown as black, red, and blue balls, respectively. Hydrogen bonds are indicated as dashed lines, with lengths given in Å. d, Close-up view of the ADD–CD interface. Critical residues for the interactions are shown in stick representation, and hydrogen bonds are indicated as dashed lines. The C terminus (residues 903–911) of the CD domain and a loop region (residues 621–632) together form a flat patch for interaction with the ADD domain. Hydrogen bonds are formed between residues N551, N553, and R556 of the ADD domain and residues E629, C911, and E907 of the CD domain. Residues Y526, Y528, W601, and F609 of the ADD domain, V622 and P625 of the linker, and R803 and P904 of the CD domain are involved in hydrophobic interactions. e, Structural comparison of ADD–CD–H3 in ADD–CD–C^DNMT3L–H3 (this study) and DNMT3L–H3 structures (PDB accession number 2PVC)¹⁵. Two compared structures are shown in ribbon representations with ADD domains (left) or catalytic domains (right) aligned, respectively. The DNMT3L–H3 structure is coloured in grey. When the ADD domains are superimposed, the catalytic domain moves with a longest distance of 19 Å. When the CD domains are superimposed, the ADD domain moves 6 Å. f, Close-up view of the H3–ADD interface. Critical residues for the interactions are shown in stick representation, and hydrogen bonds are indicated as dashed lines. The fashion of histone H3–ADD interaction is similar to that observed in the structure of the H3–ADD fusion protein¹⁶. g, Histone H3 peptide pull-down assay. Recombinant wild-type and mutant ADD–CD–C^DNMT3L proteins were incubated with biotinylated histone H3 peptide (residues 1–21) and immobilized onto streptavidin sepharose beads. Bound proteins were subjected to SDS–PAGE and stained by Coomassie blue.