› 5u5t

X-ray diffraction
1.6Å resolution

Crystal structure of EED in complex with H3K27Me3 peptide and 3-(benzo[d][1,3]dioxol-4-ylmethyl)piperidine-1-carboximidamide

Released:
DOI: 10.2210/pdb5u5t/pdb
PDB entry 5u5t coloured by chain, front view.
PDB entry 5u5t coloured by chain, side view.
PDB entry 5u5t coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase.
Lingel A, Sendzik M, Huang Y, Shultz MD, Cantwell J, Dillon MP, Fu X, Fuller J, Gabriel T, Gu J, Jiang X, Li L, Liang F, McKenna M, Qi W, Rao W, Sheng X, Shu W, Sutton J, Taft B, Wang L, Zeng J, Zhang H, Zhang M, Zhao K, Lindvall M, Bussiere DE
J Med Chem 60 415-427 (2017)
PMID: 27992714

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(27) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(27)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-131031 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Polycomb protein EED Chains: A, B
Molecule details ›
Chains: A, B
Length: 367 amino acids
Theoretical weight: 42.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: O75530 (Residues: 76-441; Coverage: 83%)
Gene name: EED
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Histone-lysine N-methyltransferase EZH2 Chains: C, D
Molecule details ›
Chains: C, D
Length: 30 amino acids
Theoretical weight: 3.75 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q15910 (Residues: 39-68; Coverage: 4%)
Gene names: EZH2, KMT6
Sequence domains: WD repeat binding protein EZH2

Ligands and Environments

2 bound ligands:
Ligand 7W7 2 x 7W7
Ligand YT3 2 x YT3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P21212
Unit cell:
a: 92.81Å b: 177.909Å c: 50.34Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.2
Expression systems:
  • Escherichia coli K-12
  • Not provided

Quick links

Citations

11 review citations

Inhibitors of Protein Methyltransferases and Demethylases.
Kaniskan et al. (2018)
10 more

1 mention without citation

Polycomb Repressive Complex 2 Modulation through the Development of EZH2-EED Interaction Inhibitors and EED Binders.
Tomassi et al. (2021)