Figure 4.

Crystal structure of the SUVH5 SRA domain bound to methylated CHH DNA. (A) Sequence of the complementary methylated CHH 10-mer (with a 3′-T overhang) containing a 5′-5mCCT step on the top strand and a 5′-AGG step opposite it on the bottom strand toward the center of the duplex. In essence, a 5mC is positioned opposite a G. (B) Stick (DNA) and ribbon (protein) representation of the 2.75 Å crystal structure of the 2:1 SUVH5 SRA–methylated CHH DNA duplex complex. The color coding is the same as in Figure 2B. Note that the 5mC5 and the G6 from the same base pair simultaneously flip out of the DNA duplex through the minor groove and are positioned in binding pockets of individual SRA domains. (C) Interaction of the flipped-out G6 in a syn conformation with residues lining the binding pocket in the structure of the complex. (D) Insertion of the syn G6 (space-filling representation) into the binding pocket of the SRA domain (electrostatic surface presentation). (E) Relative alignments of the inserted Gln392 residues that are positioned opposite each other in the structure of the complex. Note that the side chain of the Gln392 residue is sandwiched between two bases.