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 1.1 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 

  • 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 ...

    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 D3 A258Homo 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)
Find proteins for P61077 (Homo sapiens)
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PHAROS:  P61077
Find proteins for A0A386IN42 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BRCA1-associated RING domain protein 1 B115Homo sapiensMutation(s): 0 
Gene Names: BARD1
EC: 2.3.2.27
Find proteins for Q99728 (Homo sapiens)
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PHAROS:  Q99728
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 2-A Nn133Homo sapiensMutation(s): 0 
Gene Names: H2AC18H2AFOHIST2H2AAHIST2H2AA3H2AC19HIST2H2AA4
Find proteins for Q6FI13 (Homo sapiens)
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PHAROS:  Q6FI13
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-K Oo125Homo sapiensMutation(s): 0 
Gene Names: H2BC12H2BFTHIRIP1HIST1H2BK
Find proteins for O60814 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2 Pp135Homo sapiensMutation(s): 1 
Gene Names: H3C15HIST2H3AH3C14H3F2H3FMHIST2H3CH3C13HIST2H3D
Find proteins for Q71DI3 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4 Qq102Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 7
MoleculeChainsLengthOrganismImage
Widom 601 153-bpX153synthetic construct
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Entity ID: 8
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Widom 601 153-bpY153synthetic construct
Experimental Data & Validation

Experimental Data

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

Structure Validation

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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 

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