Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A6B2C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 245.92 kDa 
• Atom Count: 14339 
• Residue Count: 1371 
• 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

• DOI: 10.2210/pdb7JZV/pdb
• EMDataResource: EMD-22581

• 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 

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)
Find proteins for P61077 (Homo sapiens) Explore P61077  Go to UniProtKB:  P61077
NIH Common Fund Data Resources
PHAROS:  P61077 GTEx:  ENSG00000109332
Find proteins for A0A386IN42 (Homo sapiens) Explore A0A386IN42  Go to UniProtKB:  A0A386IN42

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
Find proteins for Q99728 (Homo sapiens) Explore Q99728  Go to UniProtKB:  Q99728
NIH Common Fund Data Resources
PHAROS:  Q99728 GTEx:  ENSG00000138376

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 2-A	N, n	133	Homo sapiens	Mutation(s): 0  Gene Names: H2AC18, H2AFO, HIST2H2AA, HIST2H2AA3, H2AC19, HIST2H2AA4
Find proteins for Q6FI13 (Homo sapiens) Explore Q6FI13  Go to UniProtKB:  Q6FI13
NIH Common Fund Data Resources
PHAROS:  Q6FI13 GTEx:  ENSG00000203812ENSG00000272196

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

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	P, p	135	Homo sapiens	Mutation(s): 1  Gene Names: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3  Go to UniProtKB:  Q71DI3
NIH Common Fund Data Resources
PHAROS:  Q71DI3 GTEx:  ENSG00000183598ENSG00000203811ENSG00000203852

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	Q, 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
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS:  P62805 GTEx:  ENSG00000274618ENSG00000197238ENSG00000197837ENSG00000158406ENSG00000278705ENSG00000197061ENSG00000270882ENSG00000270276ENSG00000273542ENSG00000277157ENSG00000276966ENSG00000276180ENSG00000278637ENSG00000275126

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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, 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