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TitleMolecular architecture of nucleosome remodeling and deacetylase sub-complexes by integrative structure determination.
Journal, issue, pagesProtein Sci, Vol. 31, Issue 9, Page e4387, Year 2022
Publish dateSep 2, 2022
AuthorsShreyas Arvindekar / Matthew J Jackman / Jason K K Low / Michael J Landsberg / Joel P Mackay / Shruthi Viswanath /
PubMed AbstractThe 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 ...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 -HDAC1-MBD3 , 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 -MTA1 , MTA1 -MBD3 , and HDAC1 -MBD3 . Our approach also allowed us to localize regions of unknown structure, such as HDAC1 and MBD3 , thereby resulting in the most complete and robustly cross-validated structural characterization of these NuRD sub-complexes so far.
External linksProtein Sci / PubMed:36040254 / PubMed Central
MethodsEM (single particle)
Resolution26.0 Å
Structure data

EMDB-27557: Negative stain EM map of an MTA-HDAC-RBBP4 complex
Method: EM (single particle) / Resolution: 26.0 Å

Source
  • Homo sapiens (human)

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