Extended Data Fig. 6: Structural basis of TNRC18BAH binding to H3K9me3 peptide and biochemical analysis of TNRC18BAH binding to H3Kc9me3-modified nucleosome.
From: TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons
a. Crystal structures of the two color-coded human TNRC18BAH molecules in one asymmetric unit, with the chain identifiers labeled (chain A and B). Each TNRC18BAH molecule is complexed with one H3K9me3 peptide (chain C or D). The TNRC18BAH-H3K9me3 complex with the best model-to-map fit (chain B and D) was selected for structural analysis. b. Electrostatic surface view of human TNRC18BAH bound to the H3K9me3 (yellow sticks). (left) The Fo-Fc omit map of the H3K9me3 peptide, contoured at 1.5σ level, is shown as magenta mesh. (right) The surface patch enriched with basic residues is indicated as the potential binding site to nucleosome/DNA. c. ITC binding curves of TNRC18BAH against histone peptides with the indicated modification. d. ITC binding curves of the indicated TNRC18BAH mutants against the H3K9me3 peptide. e. Structural comparison of ORC1BAH-H4K20me2 (electrostatic surface and stick representation; PDB 4DOW), DNMT1BAH1-H4K20me3 (electrostatic surface and stick representation; PDB 7LMK) and BAHCC1BAH-H3K27me3 (ribbon and stick representation; PDB 6VIL). f. Structural superposition of TNRC18BAH with the nucleosome core particle (NCP)-bound yeast Sir3 BAH domain (Sir3BAH; PDB 4KUD) reveals that the basic patch of TNRC18BAH (Extended Data Fig. 6b, right panel) corresponds to a similar region of Sir3BAH involved in binding to the acidic patch of NCP. g. Assessment of purified H3Kc9me3-modified NCP on a native 5% TBE gel. The positions of reconstituted NCP and biotinylated 601 DNA are labeled on the right. h. The BLI kinetic curves for the TNRC18BAH-NCP binding. The concentrations of TNRC18BAH used for each kinetic measurement are indicated. The Kd value and s.d. were derived from two independent measurements.
