5WUK

Crystal structure of EED [G255D] in complex with EZH2 peptide and EED226 compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Split luciferase-based biosensors for characterizing EED binders

Li, L.Feng, L.Shi, M.Zeng, J.Chen, Z.Zhong, L.Huang, L.Guo, W.Huang, Y.Qi, W.Lu, C.Li, E.Zhao, K.Gu, J.

(2017) Anal. Biochem. 522: 37-45

  • DOI: 10.1016/j.ab.2017.01.014

  • PubMed Abstract: 
  • The EED (embryonic ectoderm development) subunit of the Polycomb repressive complex 2 (PRC2) plays an important role in the feed forward regulation of the PRC2 enzymatic activity. We recently identified a new class of allosteric PRC2 inhibitors that ...

    The EED (embryonic ectoderm development) subunit of the Polycomb repressive complex 2 (PRC2) plays an important role in the feed forward regulation of the PRC2 enzymatic activity. We recently identified a new class of allosteric PRC2 inhibitors that bind to the H3K27me3 pocket of EED. Multiple assays were developed and used to identify and characterize this type of PRC2 inhibitors. One of them is a genetically encoded EED biosensor based on the EED[G255D] mutant and the split firefly luciferase. This EED biosensor can detect the compound binding in the transfected cells and in the in vitro biochemical assays. Compared to other commonly used cellular assays, the EED biosensor assay has the advantage of shorter compound incubation with cells. The in vitro EED biosensor is much more sensitive than other label-free biophysical assays (e.g. DSF, ITC). Based on the crystal structure, the DSF data as well as the biosensor assay data, it's most likely that compound-induced increase in the luciferase activity of the EED[G255D] biosensor results from the decreased non-productive interactions between the EED subdomain and other subdomains within the biosensor construct. This new insight of the mechanism might help to broaden the use of the split luciferase based biosensors.


    Organizational Affiliation

    China Novartis Institutes for Biomedical Research, 4218 Jinke Road, Shanghai 201203, China. Electronic address: Justin.gu@novartis.com.,China Novartis Institutes for Biomedical Research, 4218 Jinke Road, Shanghai 201203, China. Electronic address: ling-1.li@novartis.com.,China Novartis Institutes for Biomedical Research, 4218 Jinke Road, Shanghai 201203, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polycomb protein EED
A
366Homo sapiensMutation(s): 1 
Gene Names: EED
Find proteins for O75530 (Homo sapiens)
Go to Gene View: EED
Go to UniProtKB:  O75530
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase EZH2
B
28Homo sapiensMutation(s): 0 
Gene Names: EZH2 (KMT6)
EC: 2.1.1.43
Find proteins for Q15910 (Homo sapiens)
Go to Gene View: EZH2
Go to UniProtKB:  Q15910
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
73K
Query on 73K

Download SDF File 
Download CCD File 
A
N-(furan-2-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine
C17 H15 N5 O3 S
DYIRSNMPIZZNBK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
73KKd: 14 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.100α = 90.00
b = 80.280β = 90.00
c = 108.420γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-12-19 
  • Released Date: 2017-05-03 
  • Deposition Author(s): Chen, Z.

Revision History 

  • Version 1.0: 2017-05-03
    Type: Initial release