Structural insights into specific recognition of the histone variant H2A.Z by the YL1 subunit of SRCAP chromatin-remodeling complex

The SNF2-related CREB-binding protein activator protein complex regulates gene transcription through chromatin remodeling, where the subunit YL1 mediates the exchange of H2A-H2B dimers with H2A.Z-H2B in the nucleosome. Although structures of YL1 in complex with H2A.Z-H2B have been previously reported for both Drosophila and Homo sapiens, the complex structures of the two species exhibit significant differences, which have caused some confusion over how YL1 recruits H2A.Z-H2B. We determined the high-resolution (2.01 Å) crystal structure of the N-terminal region (8-73) of the human SNF2-related CREB-binding protein activator protein subunit YL1 in complex with H2B-H2A.Z; this domain is termed as YL1-Z. YL1-Z consists of an alpha helix and a longer loop, which bind to H2A.Z-H2B to form a complex. In the structure, residues Phe29, Tyr30, Tyr34, and Phe37 of the YL1-Z domain specifically recognize the hydrophobic residues, Gln87, Ile90, Ile100, and Ile104, of H2A.Z through hydrophobic interactions, forming a hydrophobic core. In addition, residues Asp55, Asp58, and Asp60 of YL1-Z form electrostatic interactions with Arg34 and Lys37 on H2A.Z, stabilizing the complex structure. The particular recognition has been validated in vitro by maltose-binding protein-pulldown and isothermal titration calorimetry experiments. Our data show that YL1 employs a conserved structural mechanism for recognizing the H2A.Z-H2B dimer.