Structural insights into the specific recognition of H2A.Z-H2B dimer by the catalytic subunit of SRCAP chromatin remodeling complex

Abstract

Chromatin remodeling complexes (SRCAP-C) mediate the exchange of H2A.Z with H2A, leading to the incorporation of H2A.Z-H2B dimers into chromatin through a step-by-step manner. Here, we determined the crystal structure of the N-terminal region (531-560) of the catalytic subunit of SRCAP-C, termed SRCAP-Z domain, in complex with the engineered single-chain H2B-H2A.Z (scH2B-H2A.Z) at 2.53 [A] resolution. In the crystal structure, two molecules of scH2B-H2A.Z and one molecule of SRCAP-Z form a sandwich-like architecture. Histones form typical histone fold and SRCAP-Z domain adopts a short 310 helix. In details, Val551, Leu554, and Leu555 of the SRCAP-Z 310 helix specifically recognize the C helix of H2A.Z through hydrophobic interactions. The particular recognition has been validated in vitro by MBP-pulldown and isothermal titration calorimetry (ITC) experiments, and the MBP-pulldown assay results demonstrated that mutations in specific amino acids of SRCAP-Z attenuated its interaction with H2A.Z-H2B dimer. Finally, we demonstrated that SRCAP-Z recognizes H2A.Z-H2B dimer with a conservative structural basis and facilitates the nucleosome assembly by its chaperone activity. HighlightsFirstly, we determined the structure of the SRCAP-Z domain/scH2A.Z-H2B complex at 2.53 [A] resolution. Second, our results support a mechanism of H2A.Z-H2B/H2A-H2B exchange model in which YL1 enriches H2A.Z/H2B around nucleosomes, presenting them to SRCAP, which mediates the exchange of H2A.Z/H2B with H2A/H2B. Third, SRCAP-Z recognition of H2A.Z-H2B dimer is structurally conserved. Fourth, a distinct sandwich-like architecture: SRCAP-Z adopts a 310 helix that inserts precisely between H2A.Z and H2B, forming a stable, unexpected structural module.