Molecular architecture of nucleosome remodeling and deacetylase sub‐complexes by integrative structure determination

Abstract

The nucleosome remodeling and deacetylase (NuRD) complex is a chromatin‐modifying assembly that regulates gene expression and DNA damage repair. Despite its importance, limited structural information describing the complete NuRD complex is available and a detailed understanding of its mechanism is therefore lacking. Drawing on information from SEC‐MALLS, DIA‐MS, XLMS, negative‐stain EM, X‐ray crystallography, NMR spectroscopy, secondary structure predictions, and homology models, we applied Bayesian integrative structure determination to investigate the molecular architecture of three NuRD sub‐complexes: MTA1‐HDAC1‐RBBP4, MTA1 N ‐HDAC1‐MBD3 GATAD2CC , and MTA1‐HDAC1‐RBBP4‐MBD3‐GATAD2A [nucleosome deacetylase (NuDe)]. The integrative structures were corroborated by examining independent crosslinks, cryo‐EM maps, biochemical assays, known cancer‐associated mutations, and structure predictions from AlphaFold. The robustness of the models was assessed by jack‐knifing. Localization of the full‐length MBD3, which connects the deacetylase and chromatin remodeling modules in NuRD, has not previously been possible; our models indicate two different locations for MBD3, suggesting a mechanism by which MBD3 in the presence of GATAD2A asymmetrically bridges the two modules in NuRD. Further, our models uncovered three previously unrecognized subunit interfaces in NuDe: HDAC1 C ‐MTA1 BAH , MTA1 BAH ‐MBD3 MBD , and HDAC1 60–100 ‐MBD3 MBD . Our approach also allowed us to localize regions of unknown structure, such as HDAC1 C and MBD3 IDR , thereby resulting in the most complete and robustly cross‐validated structural characterization of these NuRD sub‐complexes so far.