Fig. 4: Cryo-EM structure of the DIM2-HP1-H3K9me3-DNA complex.
From: Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation
a DNA sequence used for structural study. b Cryo-EM density map for the DIM2-HP1-H3K9me3-DNA complex in two opposite views. The individual domains of DIM2 are color coded. HP1, H3K9me3, and DNA are colored in magenta, lime green, and purple, respectively. c Atomic model of the DIM2-bound DNA and the corresponding density map (gray). The flipped-out zebularine Z7 is colored hot pink. d Atomic model of the DIM2-HP1-H3K9me3-DNA complex, with individual components colored in the same fashion as in (b). The SAH molecule and zinc ion are shown in sphere representation. e Close-up view of the flipped-out Z7 bound to DIM2 residues. The hydrogen bonds are depicted as red dashed lines. f Electrostatic surface view of DIM2 bound to HP1, H3K9me3 and DNA. Close-up view of H3K9me3 peptide bound to DIM2 RFTS (g) or BAH1 domain (h), with the atomic model of the histone peptide covered in the corresponding density map in black mesh and DIM2 shown in electrostatic surface representation.
