› 8t9g

Electron Microscopy
6.2Å resolution

Automethylated PRC2 dimer bound to nucleosome

Released:
DOI: 10.2210/pdb8t9g/pdb
PDB entry 8t9g coloured by chain, front view.
PDB entry 8t9g coloured by chain, side view.
PDB entry 8t9g coloured by chain, top view.
Source organisms:
Primary publication:
Activation of automethylated PRC2 by dimerization on chromatin.
Sauer PV, Pavlenko E, Cookis T, Zirden LC, Renn J, Singhal A, Hunold P, Hoehne-Wiechmann MN, van Ray O, Kaschani F, Kaiser M, Hänsel-Hertsch R, Sanbonmatsu KY, Nogales E, Poepsel S
Mol Cell (2024)
PMID: 39303719
Related structures: EMD-41110

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:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 21-mer (preferred)
PDBe Complex ID:
PDB-CPX-275844 (preferred)
Entry contents:
10 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (12 distinct):
Polycomb protein SUZ12 Chains: B, G
Molecule details ›
Chains: B, G
Length: 619 amino acids
Theoretical weight: 72.27 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q15022 (Residues: 68-685; Coverage: 84%)
Gene names: CHET9, JJAZ1, KIAA0160, SUZ12
Sequence domains: VEFS-Box of polycomb protein
Histone-lysine N-methyltransferase EZH2 Chains: C, I
Molecule details ›
Chains: C, I
Length: 753 amino acids
Theoretical weight: 86.17 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q15910 (Residues: 2-297, 298-746; Coverage: 100%)
  • Best match: Q15910-2 (Residues: 2-751)
Gene names: EZH2, KMT6
Sequence domains:
Polycomb protein EED Chains: F, K
Molecule details ›
Chains: F, K
Length: 441 amino acids
Theoretical weight: 50.27 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O75530 (Residues: 1-441; Coverage: 100%)
Gene name: EED
Sequence domains: WD domain, G-beta repeat
Histone-binding protein RBBP4 Chains: L, O
Molecule details ›
Chains: L, O
Length: 425 amino acids
Theoretical weight: 47.71 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q09028 (Residues: 1-425; Coverage: 100%)
Gene names: RBAP48, RBBP4
Sequence domains:
Zinc finger protein AEBP2 Chains: M, Y
Molecule details ›
Chains: M, Y
Length: 303 amino acids
Theoretical weight: 34.18 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6ZN18 (Residues: 223-517; Coverage: 57%)
  • Best match: Q6ZN18-3 (Residues: 1-301)
Gene name: AEBP2
Histone H3.2 Chains: A, W
Molecule details ›
Chains: A, W
Length: 136 amino acids
Theoretical weight: 15.44 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: J, X
Molecule details ›
Chains: J, X
Length: 106 amino acids
Theoretical weight: 11.63 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: R, U
Molecule details ›
Chains: R, U
Length: 133 amino acids
Theoretical weight: 14.36 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 1-130; Coverage: 100%)
Sequence domains:
Histone H2B 1.1 Chains: S, V
Molecule details ›
Chains: S, V
Length: 123 amino acids
Theoretical weight: 13.66 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
Sequence domains: Core histone H2A/H2B/H3/H4
activating methylated peptide Chain: E
Molecule details ›
Chain: E
Length: 12 amino acids
Theoretical weight: 1.13 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
DNA (226-MER) Chain: H
Molecule details ›
Chain: H
Length: 215 nucleotides
Theoretical weight: 66.54 KDa
DNA (226-MER) Chain: T
Molecule details ›
Chain: T
Length: 215 nucleotides
Theoretical weight: 65.91 KDa

Ligands and Environments

1 bound ligand:
Ligand SAH 2 x SAH
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
Resolution: 6.2Å
Relevant EMDB volumes: EMD-41110
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

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