7AO9

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The topology of chromatin-binding domains in the NuRD deacetylase complex.

Millard, C.J., Fairall, L., Ragan, T.J., Savva, C.G., Schwabe, J.W.R.

(2020) Nucleic Acids Res 48: 12972-12982

  • DOI: 10.1093/nar/gkaa1121
  • Primary Citation of Related Structures:  
    7AOA, 7AO8, 7AO9

  • 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 ...

    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.

    Organizational Affiliation: 

    The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methyl-CpG-binding domain protein 2A [auth C]411Homo sapiensMutation(s): 0 
Gene Names: MBD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBB5 (Homo sapiens)
Explore Q9UBB5 
Go to UniProtKB:  Q9UBB5
PHAROS:  Q9UBB5
GTEx:  ENSG00000134046
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Metastasis-associated protein MTA1D [auth A], B [auth D]715Homo sapiensMutation(s): 0 
Gene Names: MTA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13330 (Homo sapiens)
Explore Q13330 
Go to UniProtKB:  Q13330
PHAROS:  Q13330
GTEx:  ENSG00000182979
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 1E [auth B], C [auth E]482Homo sapiensMutation(s): 0 
Gene Names: HDAC1, RPD3L1
EC: 3.5.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for Q13547 (Homo sapiens)
Explore Q13547 
Go to UniProtKB:  Q13547
PHAROS:  Q13547
GTEx:  ENSG00000116478
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWT100237/Z/12/Z
Medical Research Council (MRC, United Kingdom)United KingdomMC_PC_17136
Wolfson FoundationUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Database references