8T3W

Structure of Bre1-nucleosome complex - state2

• PDB DOI: https://doi.org/10.2210/pdb8T3W/pdb
• EM Map EMD-41015: EMDB EMDataResource
• NAKB: 8T3W

• Classification: DNA BINDING PROTEIN/Transferase/DNA
• Organism(s): Xenopus laevis, synthetic construct, Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-06-07 Released: 2023-10-18 
• Deposition Author(s): Zhao, F., Hicks, C.W., Wolberger, C.
• 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: 3.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanism of histone H2B monoubiquitination by Bre1.

Zhao, F., Hicks, C.W., Wolberger, C.

(2023) Nat Struct Mol Biol 30: 1623-1627

• PubMed: 37872231 
• DOI: https://doi.org/10.1038/s41594-023-01137-x
• Primary Citation of Related Structures:  
  8T3T, 8T3W, 8T3Y


• PubMed Abstract: 
  

  Monoubiquitination of histone H2B-K120/123 plays several roles in regulating transcription, DNA replication and the DNA damage response. The structure of a nucleosome in complex with the dimeric RING E3 ligase Bre1 reveals that one RING domain binds to the nucleosome acidic patch, where it can position the E2 ubiquitin conjugating enzyme Rad6, while the other RING domain contacts the DNA. Comparisons with H2A-specific E3 ligases suggest a general mechanism of tuning histone specificity via the non-E2-binding RING domain.

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Organizational Affiliation: 

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A6B2C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - E2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 223.8 kDa 
• Atom Count: 13,001 
• Modelled Residue Count: 1,178 
• Deposited Residue Count: 1,488 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	135	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	102	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	C, G	129	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897  Go to UniProtKB:  P06897

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	122	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase BRE1	K, L	110	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: BRE1, YDL074C EC: 2.3.2.27
UniProt
Find proteins for Q07457 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q07457  Go to UniProtKB:  Q07457

Entity ID: 5
Molecule	Chains	Length	Organism	Image
601 DNA strand 1	I	146	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
601 DNA strand 2	J	146	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	M [auth K], N [auth K], O [auth L], P [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1
MODEL REFINEMENT	Coot	0.8.9.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Zhao, F., Hicks, C.W., Wolberger, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM130393

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Database references
• Version 1.3: 2023-11-22
  Changes: Database references