7AO9

Structure of the core MTA1/HDAC1/MBD2 NURD deacetylase complex

Summary for 7AO9

• Entry DOI: 10.2210/pdb7ao9/pdb
• EMDB information: 11837 11838 11839 3399
• Descriptor: Methyl-CpG-binding domain protein 2, Metastasis-associated protein MTA1, Histone deacetylase 1, ... (6 entities in total)
• Functional Keywords: deacetylase, complex, transcription
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 5
• Total formula weight: 317097.34

Authors

Millard, C.J.,Fairall, L.,Ragan, T.J.,Savva, C.G.,Schwabe, J.W.R. (deposition date: 2020-10-14, release date: 2020-11-11, Last modification date: 2024-05-01)

Primary citation

Millard, C.J.,Fairall, L.,Ragan, T.J.,Savva, C.G.,Schwabe, J.W.R.
The topology of chromatin-binding domains in the NuRD deacetylase complex.
Nucleic Acids Res., 48:12972-12982, 2020

PubMed Abstract: Class I histone deacetylase complexes play essential roles in many nuclear processes. Whilst they contain a common catalytic subunit, they have diverse modes of action determined by associated factors in the distinct complexes. The deacetylase module from the NuRD complex contains three protein domains that control the recruitment of chromatin to the deacetylase enzyme, HDAC1/2. Using biochemical approaches and cryo-electron microscopy, we have determined how three chromatin-binding domains (MTA1-BAH, MBD2/3 and RBBP4/7) are assembled in relation to the core complex so as to facilitate interaction of the complex with the genome. We observe a striking arrangement of the BAH domains suggesting a potential mechanism for binding to di-nucleosomes. We also find that the WD40 domains from RBBP4 are linked to the core with surprising flexibility that is likely important for chromatin engagement. A single MBD2 protein binds asymmetrically to the dimerisation interface of the complex. This symmetry mismatch explains the stoichiometry of the complex. Finally, our structures suggest how the holo-NuRD might assemble on a di-nucleosome substrate.

PubMed: 33264408
DOI: 10.1093/nar/gkaa1121

Experimental method

ELECTRON MICROSCOPY (6.1 Å)