Supplementary Figure 4: YL1 ZIDN has the ability to interact with H2A.Z–H2B through an arginine anchor feature.
From: Molecular basis and specificity of H2A.Z–H2B recognition and deposition by the histone chaperone YL1
a) Dimer of the YL1–ZID–H2A.Z–H2B complex observed in the crystal, where dimerization occurs through stacking of YL1 αN1 helices. At this dimeric interface, the N-terminal region of the YL1–ZID (ZIDN) from one complex interacts with the H2A.Z–H2B pair from a symmetry-related YL1–ZID–H2A.Z–H2B complex. This interaction between the ZIDN and the H2A.Z–H2B pair includes an arginine anchor, where an YL1 arginine binds to the acidic patch pocket of H2A.Z. This interaction is reminiscent of interactions made by several transcription and epigenetic effectors when bound to the nucleosome. In addition, ZIDN conserved residues are involved in this interaction that is only possible due to the presence of H2A.Z-specific G92 (an asparagine in H2A), enabling YL1–ZIDN to lay onto H2A.Z.
b) Examples of arginine anchor features. Upper left: RingIB (from PCR1 complex) binding to the H2A nucleosome (PDB code 4R8P). Bottom: RCC1 binding to the H2A nucleosome (PDB code 3MVD). Upper right: YL1–ZIDN binding to H2A.Z (this study). The position of H2A N89 and equivalent H2A.Z G92 are displayed, showing that the presence of a bulkier side chain at this position affects the way of binding of the effectors to H2A/H2A.Z.
c) Stereo view of the Fo–Fc simulated-annealing omit map contoured at 2.5 σ of H2A.Z α2 helix C-terminus and L2 loop in the YL1–ZID–H2A.Z–H2B complex. Residues spanning this region were removed prior to simulated-annealing.
