PDBe 5hyn

X-ray diffraction
2.95Å resolution

Structure of Human Polycomb Repressive Complex 2 (PRC2) with oncogenic histone H3K27M peptide

Released:

Function and Biology Details

Reaction catalysed:
S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assemblies composition:
hetero pentamer (preferred)
hetero tetramer
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Histone-lysine N-methyltransferase EZH2 Chains: A, F, K, Q
Molecule details ›
Chains: A, F, K, Q
Length: 746 amino acids
Theoretical weight: 85.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15910 (Residues: 1-746; Coverage: 100%)
Gene names: EZH2, KMT6
Sequence domains:
Polycomb protein EED Chains: B, G, L, R
Molecule details ›
Chains: B, G, L, R
Length: 367 amino acids
Theoretical weight: 42.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O75530 (Residues: 77-441; Coverage: 83%)
Gene name: EED
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Polycomb protein SUZ12 Chains: C, H, M, S
Molecule details ›
Chains: C, H, M, S
Length: 129 amino acids
Theoretical weight: 15.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15022 (Residues: 558-685; Coverage: 17%)
Gene names: CHET9, JJAZ1, KIAA0160, SUZ12
Histone H3.1 Chains: D, I, O, T
Molecule details ›
Chains: D, I, O, T
Length: 13 amino acids
Theoretical weight: 1.23 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 22-34; Coverage: 10%)
Gene names: H3FA, H3FB, H3FC, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J
Protein Jumonji Chains: E, J, P, U
Molecule details ›
Chains: E, J, P, U
Length: 12 amino acids
Theoretical weight: 1.51 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q92833 (Residues: 110-121; Coverage: 1%)
Gene names: JARID2, JMJ

Ligands and Environments


Cofactor: Ligand SAH 4 x SAH
1 bound ligand:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 131.64Å b: 171.51Å c: 274.55Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.219 0.273
Expression systems:
  • Escherichia coli
  • Not provided