7LYC

Cryo-EM structure of the human nucleosome core particle ubiquitylated at histone H2A Lys13 and Lys15 in complex with BARD1 (residues 415-777)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Mechanisms of BRCA1-BARD1 nucleosome recognition and ubiquitylation.

Hu, Q., Botuyan, M.V., Zhao, D., Cui, G., Mer, E., Mer, G.

(2021) Nature 596: 438-443

  • DOI: https://doi.org/10.1038/s41586-021-03716-8
  • Primary Citation of Related Structures:  
    7LYA, 7LYB, 7LYC

  • PubMed Abstract: 

    • The BRCA1-BARD1 tumour suppressor is an E3 ubiquitin ligase necessary for the repair of DNA double-strand breaks by homologous recombination 1-10 . The BRCA1-BARD1 complex localizes to damaged chromatin after DNA replication and catalyses the ubiquitylation of histone H2A and other cellular targets 11-14 ...

    The BRCA1-BARD1 tumour suppressor is an E3 ubiquitin ligase necessary for the repair of DNA double-strand breaks by homologous recombination 1-10 . The BRCA1-BARD1 complex localizes to damaged chromatin after DNA replication and catalyses the ubiquitylation of histone H2A and other cellular targets 11-14 . The molecular bases for the recruitment to double-strand breaks and target recognition of BRCA1-BARD1 remain unknown. Here we use cryo-electron microscopy to show that the ankyrin repeat and tandem BRCT domains in BARD1 adopt a compact fold and bind to nucleosomal histones, DNA and monoubiquitin attached to H2A amino-terminal K13 or K15, two signals known to be specific for double-strand breaks 15,16 . We further show that RING domains 17 in BRCA1-BARD1 orient an E2 ubiquitin-conjugating enzyme atop the nucleosome in a dynamic conformation, primed for ubiquitin transfer to the flexible carboxy-terminal tails of H2A and variant H2AX. Our work reveals a regulatory crosstalk in which recognition of monoubiquitin by BRCA1-BARD1 at the N terminus of H2A blocks the formation of polyubiquitin chains and cooperatively promotes ubiquitylation at the C terminus of H2A. These findings elucidate the mechanisms of BRCA1-BARD1 chromatin recruitment and ubiquitylation specificity, highlight key functions of BARD1 in both processes and explain how BRCA1-BARD1 promotes homologous recombination by opposing the DNA repair protein 53BP1 in post-replicative chromatin 18-22 . These data provide a structural framework to evaluate BARD1 variants and help to identify mutations that drive the development of cancer.

    Organizational Affiliation: 

    Department of Cancer Biology, Mayo Clinic, Rochester, MN, USA. mer.georges@mayo.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1A,
D [auth E]		140Homo sapiensMutation(s): 0 
Gene Names: 
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PHAROS:  P68431
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UniProt GroupP68431
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B,
E [auth F]		107Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JC [auth D],
F [auth H]		126Homo sapiensMutation(s): 0 
Gene Names: H2BC11, H2BFR, HIST1H2BJ
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinI [auth K]84Homo sapiensMutation(s): 0 
Gene Names: UBB
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
BRCA1-associated RING domain protein 1J [auth N]373Homo sapiensMutation(s): 0 
Gene Names: BARD1
EC: 2.3.2.27
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Find proteins for Q99728 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EK [auth C],
L [auth G]		119Homo sapiensMutation(s): 0 
Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (147-MER)G [auth I]147Homo sapiens
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (146-MER)H [auth J]147Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2-3874
RECONSTRUCTIONcryoSPARC2.15

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA132878
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM136262
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM116829

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references
  • Version 1.2: 2021-08-25
    Changes: Database references
  • Version 1.3: 2021-09-01
    Changes: Database references