Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A6B2C1D1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 245.92 kDa 
• Atom Count: 14339 
• Modelled Residue Count: 1371 
• Deposited Residue Count: 1669 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

7JZV

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

• PDB DOI: 10.2210/pdb7JZV/pdb
• EM Map EMD-22581:EMDBEMDataResource

• Classification: LIGASE/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-09-02 Released: 2021-02-17 
• Deposition Author(s): Witus, S.R., Burrell, A.L., Hansen, J.M., Farrell, D.P., Dimaio, F., Kollman, J.M., Klevit, R.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

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

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

• PubMed: 33589814 
• 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. 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.

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Organizational Affiliation: 

Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BRCA1,Ubiquitin-conjugating enzyme E2 D3	A	258	Homo sapiens	Mutation(s): 1  Gene Names: BRCA1, UBE2D3, UBC5C, UBCH5C 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
UniProt Groups	P61077P38398

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BRCA1-associated RING domain protein 1	B	115	Homo sapiens	Mutation(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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 2-A	C [auth N], I [auth n]	133	Homo sapiens	Mutation(s): 0  Gene Names: H2AC18, H2AFO, HIST2H2AA, HIST2H2AA3, H2AC19, HIST2H2AA4
UniProt & NIH Common Fund Data Resources
Find proteins for Q6FI13 (Homo sapiens) Explore Q6FI13  Go to UniProtKB:  Q6FI13
PHAROS:  Q6FI13 GTEx:  ENSG00000203812 ENSG00000272196

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-K	D [auth O], J [auth o]	125	Homo sapiens	Mutation(s): 0  Gene Names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens) Explore O60814  Go to UniProtKB:  O60814
PHAROS:  O60814 GTEx:  ENSG00000197903

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	E [auth P], K [auth p]	135	Homo sapiens	Mutation(s): 1  Gene Names: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3  Go to UniProtKB:  Q71DI3
PHAROS:  Q71DI3 GTEx:  ENSG00000183598 ENSG00000203811 ENSG00000203852

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	F [auth Q], L [auth q]	102	Homo sapiens	Mutation(s): 0  Gene Names:  H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Entity ID: 7
Molecule	Chains	Length	Organism	Image
Widom 601 153-bp	G [auth X]	153	synthetic construct

Entity ID: 8
Molecule	Chains	Length	Organism	Image
Widom 601 153-bp	H [auth Y]	153	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	M [auth A], N [auth A], O [auth B], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-09-02 
• Released Date: 2021-02-17 
Deposition Author(s): Witus, S.R., Burrell, A.L., Hansen, J.M., Farrell, D.P., Dimaio, F., Kollman, J.M., Klevit, R.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM088055

Revision History  

• 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