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 1.3 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: https://doi.org/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. 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.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BRCA1,Ubiquitin-conjugating enzyme E2 D3258Homo 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)
UniProt & NIH Common Fund Data Resources
Find proteins for P38398 (Homo sapiens)
Explore P38398 
Go to UniProtKB:  P38398
PHAROS:  P38398
GTEx:  ENSG00000012048 
Find proteins for P61077 (Homo sapiens)
Explore P61077 
Go to UniProtKB:  P61077
PHAROS:  P61077
GTEx:  ENSG00000109332 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP61077P38398
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BRCA1-associated RING domain protein 1115Homo sapiensMutation(s): 0 
Gene Names: BARD1
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q99728 (Homo sapiens)
Explore Q99728 
Go to UniProtKB:  Q99728
PHAROS:  Q99728
GTEx:  ENSG00000138376 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99728
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 2-AC [auth N],
I [auth n]
133Homo sapiensMutation(s): 0 
Gene Names: H2AC18H2AFOHIST2H2AAHIST2H2AA3H2AC19HIST2H2AA4
UniProt & NIH Common Fund Data Resources
Find proteins for Q6FI13 (Homo sapiens)
Explore Q6FI13 
Go to UniProtKB:  Q6FI13
PHAROS:  Q6FI13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6FI13
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-KD [auth O],
J [auth o]
125Homo sapiensMutation(s): 0 
Gene Names: H2BC12H2BFTHIRIP1HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens)
Explore O60814 
Go to UniProtKB:  O60814
PHAROS:  O60814
GTEx:  ENSG00000197903 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60814
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2E [auth P],
K [auth p]
135Homo sapiensMutation(s): 1 
Gene Names: H3C15HIST2H3AH3C14H3F2H3FMHIST2H3CH3C13HIST2H3D
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens)
Explore Q71DI3 
Go to UniProtKB:  Q71DI3
PHAROS:  Q71DI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ71DI3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4F [auth Q],
L [auth q]
102Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62805
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains LengthOrganismImage
Widom 601 153-bpG [auth X]153synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains LengthOrganismImage
Widom 601 153-bpH [auth Y]153synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTRosettaEM

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
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references