8OFF

Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

BRCA1-BARD1 combines multiple chromatin recognition modules to bridge nascent nucleosomes.

Burdett, H.Foglizzo, M.Musgrove, L.J.Kumar, D.Clifford, G.Campbell, L.J.Heath, G.R.Zeqiraj, E.Wilson, M.D.

(2023) Nucleic Acids Res 51: 11080-11103

  • DOI: https://doi.org/10.1093/nar/gkad793
  • Primary Citation of Related Structures:  
    8OFF

  • PubMed Abstract: 

    Chromatin association of the BRCA1-BARD1 heterodimer is critical to promote homologous recombination repair of DNA double-strand breaks (DSBs) in S/G2. How the BRCA1-BARD1 complex interacts with chromatin that contains both damage induced histone H2A ubiquitin and inhibitory H4K20 methylation is not fully understood. We characterised BRCA1-BARD1 binding and enzymatic activity to an array of mono- and di-nucleosome substrates using biochemical, structural and single molecule imaging approaches. We found that the BRCA1-BARD1 complex preferentially interacts and modifies di-nucleosomes over mono-nucleosomes, allowing integration of H2A Lys-15 ubiquitylation signals with other chromatin modifications and features. Using high speed- atomic force microscopy (HS-AFM) to monitor how the BRCA1-BARD1 complex recognises chromatin in real time, we saw a highly dynamic complex that bridges two nucleosomes and associates with the DNA linker region. Bridging is aided by multivalent cross-nucleosome interactions that enhance BRCA1-BARD1 E3 ubiquitin ligase catalytic activity. Multivalent interactions across nucleosomes explain how BRCA1-BARD1 can recognise chromatin that retains partial di-methylation at H4 Lys-20 (H4K20me2), a parental histone mark that blocks BRCA1-BARD1 interaction with nucleosomes, to promote its enzymatic and DNA repair activities.


  • Organizational Affiliation

    Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1B [auth Ca],
H [auth Cb]
135Homo sapiensMutation(s): 0 
Gene Names: 
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UniProt GroupP68431
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-C/E/F/G/IC [auth Ba],
E [auth Bb]
126Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BCH2BFLHIST1H2BEH2BFHHIST1H2BFH2BFGHIST1H2BGH2BFAHIST1H2BIH2BFK
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Find proteins for P62807 (Homo sapiens)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1D [auth Aa],
G [auth Ab]
130Homo sapiensMutation(s): 0 
Gene Names: 
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PHAROS:  P0C0S8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4F [auth Da],
I [auth Db]
103Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
BRCA1 associated RING domain 1J [auth Ea],
L [auth Eb]
773Felis catusMutation(s): 0 
Gene Names: BARD1
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinK [auth Fa]76Homo sapiensMutation(s): 0 
Gene Names: UBC
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PHAROS:  P0CG48
GTEx:  ENSG00000150991 
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (142-MER)A [auth J],
M [auth I]
350Homo sapiens
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.17.1_3660:
RECONSTRUCTIONcryoSPARC4.0.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/T029471/1
Wellcome TrustUnited Kingdom222531/Z/21/Z
Wellcome TrustUnited Kingdom108466/Z/15/Z
Wellcome TrustUnited Kingdom221524/Z/20/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Database references