Fig. 2

The structural details of the TRIM66 PHD-Bromodomain binding the H3 N-terminal and H3K56ac peptides. a Crystal structure of the TRIM66 PHD-Bromodomain in the complex state with H3 N-terminal tail. The H3 N-terminal peptide (in yellow) interacts with the PHD finger domain (in aquamarine). Bromodomain is shown in light pink. The zinc ions are shown as silver spheres. The linker (dash line) is invisible in the structure. b Detailed interactions between the H3_1–10 peptide (in yellow) and the PHD finger of TRIM66 in the complex structure of the TRIM66 PHD-Bromodomain binding the H3 N-terminal tail. The hydrogen bonds are shown in forest green dashed lines. In b–d, several residues in the interaction between the TRIM66 PHD finger and N-terminal H3 tail are labeled and shown in sticks with red oxygen atoms, blue nitrogen atoms, and orange sulfur atoms. A water molecule mediating the H3-TRIM66 PHD interaction is shown as a small red sphere. c Electrostatic (protein) and stick (peptide) representation of the crystal structure of H3_1–10 peptide binding to the TRIM66 PHD-Bromodomain. d Detailed interactions between the H3R2 residue and the PHDs from TRIM24, TRIM33, and TRIM66. The hydrogen bonds are shown in warm pink dashed lines. TRIM24, PDB code: 3O37; TRIM33, PDB code: 3U5O; TRIM66, this study. e Close-up views of the NMR chemical shift perturbations of the ¹⁵N-labeled TRIM66 PHD-Bromodomain upon the titration of the H3K56ac peptides. The molar ratio of peptide/protein was 0:1 (red), 0.7:1 (yellow), 1.4:1 (blue), and 2.8:1 (purple). The perturbation direction is marked as the arrow and the corresponding residues are also labeled. The unassigned residues are marked as a star. f The perturbed residues were mapped and labeled on the structure of the TRIM66 PHD-Bromodomain (gray surface). Residues F1122, N1123, Y1124, and D1126 are shown in red, whereas other perturbed residues are shown in yellow