Supplementary Figure 3: Human YL1, human ANP32E and yeast SWR1 all extend the αC helix, but only YL1 entirely covers the H2A.Z–H2B DNA-binding surface.
From: Molecular basis and specificity of H2A.Z–H2B recognition and deposition by the histone chaperone YL1
a) Superposition of (left) human YL1–ZID–H2A.Z–H2B (colored violet, orange and light gray, respectively) and human ANP32E–ZID–H2A.Z–H2B (colored blue, red and gray, respectively) complexes and of (right) human ANP32E–ZID–H2A.Z–H2B (colored blue, red and gray, respectively) and yeast SWR1–Z–H2A.Z–H2B (colored green, light red and dark gray, respectively) complexes. The common regions of interaction between YL1, ANP32E and SWR1 with the H2A.Z–H2B pair are boxed and labeled (ZIDM1 and ZIDM2). All H2A.Z histone chaperones extend H2A.Z αC helix, but only YL1 interacts extensively with the variant histone pair. In addition, YL1 binds to H2A.Z α3–αC region with a different conformation that ANP32E and SWR1, these latter chaperones showing high structural similarity.
b) Superposition of YL1 αN2 (violet) and ANP32E (blue) αN helices. The side chains of the hydrophobic residues of these helices that form hydrophobic interactions with the same set of hydrophobic residues from H2A.Z and H2B are shown as sticks. These hydrophobic residues from the histone chaperones occupy the same positions explaining that despite their difference in composition and the antiparallel orientation of the YL1 αN2 and ANP32E αN helices, they have the same effect in favoring H2A.Z αC helix extension. The only exception concerns YL1 Y30 that occupies a unique position and forms an YL1-specific hydrogen bonding network with residues from YL1 and H2A.Z.
c) Ribbon representation of (left) the superposed human YL1–ZID–H2A.Z–H2B (colored violet, orange and light gray, respectively) complex and H2A.Z–H2B histone pair (not shown) bound to a nucleosomal DNA region (green) and (right) the superposed human ANP32E–ZID–H2A.Z–H2B (colored blue, red and gray, respectively) complex and H2A.Z–H2B histone pair (not shown) bound to a nucleosomal DNA region (green). The C-terminal region of the YL1–ZID completely covers the H2A.Z–H2B DNA-binding surface.
d) Surface electrostatic potential of the DNA-binding region of the H2A.Z–H2B histone dimer (–5 kBT, 5 kBT; kB, Boltzmann constant; blue: positive, red: negative). Left: The H2A.Z–H2B dimer displays a highly positive electrostatic potential in its DNA binding groove. The YL1–ZID binding to the H2A.Z–H2B dimer is displayed as ribbon. Right panel: Same as left, but with YL1–ZID included in the surface electrostatic potential calculation. Upon binding, the YL1–ZID not only covers the DNA-binding region of the H2A.Z–H2B dimer, but completely changes the electrostatic potential displayed on this face of the complex, rendering it more negative and thus, repulsive for DNA interactions.
