4R7E | pdb_00004r7e

Structure of Bre1 RING domain

• PDB DOI: https://doi.org/10.2210/pdb4R7E/pdb

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-27 Released: 2015-05-13 
• Deposition Author(s): Kumar, P., Wolberger, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.247 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Structure of the yeast Bre1 RING domain.

Kumar, P., Wolberger, C.

(2015) Proteins 83: 1185-1190

• PubMed: 25864391 
• DOI: https://doi.org/10.1002/prot.24812
• Primary Citation Related Structures: 
  4R7E


• PubMed Abstract: 
  

  Monoubiquitination of histone H2B at Lys123 in yeast plays a critical role in regulating transcription, mRNA export, DNA replication, and the DNA damage response. The RING E3 ligase, Bre1, catalyzes monoubiquitination of H2B in concert with the E2 ubiquitin-conjugating enzyme, Rad6. The crystal structure of a C-terminal fragment of Bre1 shows that the catalytic RING domain is preceded by an N-terminal helix that mediates coiled-coil interactions with a crystallographically related monomer. Homology modeling suggests that the human homologue of Bre1, RNF20/RNF40, heterodimerizes through similar coiled-coil interactions.

---

Organizational Affiliation: 
• Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland, 21205.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 8.02 kDa 
• Atom Count: 539 
• Modeled Residue Count: 69 
• Deposited Residue Count: 69 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase BRE1	A	69	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: Bre1, YDL074C EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt
Find proteins for Q07457 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q07457  Go to UniProtKB:  Q07457

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.247 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.765	α = 90
b = 56.765	β = 90
c = 134.858	γ = 120

Software Package:

Software Name	Purpose
CBF:	data collection
CBFlib	data collection
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Kumar, P., Wolberger, C.

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2015-08-26
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations