7JZV

Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1.

Witus, S.R.Burrell, A.L.Farrell, D.P.Kang, J.Wang, M.Hansen, J.M.Pravat, A.Tuttle, L.M.Stewart, M.D.Brzovic, P.S.Chatterjee, C.Zhao, W.DiMaio, F.Kollman, J.M.Klevit, R.E.

(2021) Nat Struct Mol Biol 28: 268-277

  • DOI: 10.1038/s41594-020-00556-4
  • Primary Citation of Related Structures:  
    7JZV

  • PubMed Abstract: 
  • Mutations in the E3 ubiquitin ligase RING domains of BRCA1/BARD1 predispose carriers to breast and ovarian cancers. We present the structure of the BRCA1/BARD1 RING heterodimer with the E2 enzyme UbcH5c bound to its cellular target, the nucleosome, along with biochemical data that explain how the complex selectively ubiquitylates lysines 125, 127 and 129 in the flexible C-terminal tail of H2A in a fully human system ...

    Mutations in the E3 ubiquitin ligase RING domains of BRCA1/BARD1 predispose carriers to breast and ovarian cancers. We present the structure of the BRCA1/BARD1 RING heterodimer with the E2 enzyme UbcH5c bound to its cellular target, the nucleosome, along with biochemical data that explain how the complex selectively ubiquitylates lysines 125, 127 and 129 in the flexible C-terminal tail of H2A in a fully human system. The structure reveals that a novel BARD1-histone interface couples to a repositioning of UbcH5c compared to the structurally similar PRC1 E3 ligase Ring1b/Bmi1 that ubiquitylates H2A Lys119 in nucleosomes. This interface is sensitive to both H3 Lys79 methylation status and mutations found in individuals with cancer. Furthermore, NMR reveals an unexpected mode of E3-mediated substrate regulation through modulation of dynamics in the C-terminal tail of H2A. Our findings provide insight into how E3 ligases preferentially target nearby lysine residues in nucleosomes by a steric occlusion and distancing mechanism.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA. klevit@uw.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BRCA1,Ubiquitin-conjugating enzyme E2 D3A258Homo sapiensMutation(s): 1 
Gene Names: BRCA1UBE2D3UBC5CUBCH5C
EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data), 2.3.2.27 (PDB Primary Data)
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GTEx:  ENSG00000012048 
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GTEx:  ENSG00000109332 
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UniProt GroupsP61077P38398
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BRCA1-associated RING domain protein 1B115Homo sapiensMutation(s): 0 
Gene Names: BARD1
EC: 2.3.2.27
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GTEx:  ENSG00000138376 
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UniProt GroupQ99728
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 2-AC [auth N],
I [auth n]
133Homo sapiensMutation(s): 0 
Gene Names: H2AC18H2AFOHIST2H2AAHIST2H2AA3H2AC19HIST2H2AA4
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-KD [auth O],
J [auth o]
125Homo sapiensMutation(s): 0 
Gene Names: H2BC12H2BFTHIRIP1HIST1H2BK
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GTEx:  ENSG00000197903 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2E [auth P],
K [auth p]
135Homo sapiensMutation(s): 1 
Gene Names: H3C15HIST2H3AH3C14H3F2H3FMHIST2H3CH3C13HIST2H3D
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4F [auth Q],
L [auth q]
102Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 7
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Widom 601 153-bpG [auth X]153synthetic construct
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Entity ID: 8
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Widom 601 153-bpH [auth Y]153synthetic construct
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM088055

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-17
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2021-03-24
    Changes: Database references