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 8OFF | pdb_00008off

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

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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 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.

Macromolecule Content 

  • Total Structure Weight: 506.21 kDa 
  • Atom Count: 14,424 
  • Modeled Residue Count: 1,435 
  • Deposited Residue Count: 3,310 
  • Unique protein chains: 6
  • Unique nucleic acid chains: 1

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: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
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Go to UniProtKB:  P68431
Entity Groups
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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: HIST1H2BC, H2BFL, HIST1H2BE, H2BFH, HIST1H2BF, H2BFG, HIST1H2BG, H2BFA, HIST1H2BI, H2BFK
UniProt & NIH Common Fund Data Resources
Find proteins for P62807 (Homo sapiens)
Explore P62807 
Go to UniProtKB:  P62807
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UniProt GroupP62807
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Reference Sequence
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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: 
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S8 (Homo sapiens)
Explore P0C0S8 
Go to UniProtKB:  P0C0S8
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UniProt GroupP0C0S8
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4F [auth Da],
I [auth Db]
103Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
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UniProt GroupP62805
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Reference Sequence
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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
Entity Groups
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
UbiquitinK [auth Fa]76Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
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Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
GTEx:  ENSG00000150991 
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UniProt GroupP0CG48
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (142-MER)A [auth J],
M [auth I]
350Homo sapiens
Sequence Annotations
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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