› 6c23

Electron Microscopy
3.9Å resolution

Cryo-EM structure of PRC2 bound to cofactors AEBP2 and JARID2 in the Compact Active State

Released:
DOI: 10.2210/pdb6c23/pdb
PDB entry 6c23 coloured by chain, front view.
PDB entry 6c23 coloured by chain, side view.
PDB entry 6c23 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structures of human PRC2 with its cofactors AEBP2 and JARID2.
Kasinath V, Faini M, Poepsel S, Reif D, Feng XA, Stjepanovic G, Aebersold R, Nogales E
Science 359 940-944 (2018)
PMID: 29348366
Related structures: EMD-7334

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-131024 (preferred)
Entry contents:
9 distinct polypeptide molecules
Macromolecules (9 distinct):
Polycomb protein SUZ12 Chains: A, M, Q
Molecule details ›
Chains: A, M, Q
Length: 739 amino acids
Theoretical weight: 83.18 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q15022 (Residues: 1-739; Coverage: 100%)
Gene names: CHET9, JJAZ1, KIAA0160, SUZ12
Sequence domains: VEFS-Box of polycomb protein
Protein Jumonji Chain: E
Molecule details ›
Chain: E
Length: 348 amino acids
Theoretical weight: 37.94 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q92833 (Residues: 106-450; Coverage: 28%)
Gene names: JARID2, JMJ
Histone-lysine N-methyltransferase EZH2 Chains: C, K
Molecule details ›
Chains: C, K
Length: 746 amino acids
Theoretical weight: 85.49 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q15910 (Residues: 1-746; Coverage: 100%)
Gene names: EZH2, KMT6
Sequence domains:
Polycomb protein EED Chain: L
Molecule details ›
Chain: L
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
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Histone-binding protein RBBP4 Chain: N
Molecule details ›
Chain: N
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:
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
JARID2-substrate Chain: O
Molecule details ›
Chain: O
Length: 7 amino acids
Theoretical weight: 736 Da
Source organism: Homo sapiens
Expression system: Trichoplusia ni
Zinc finger protein AEBP2 Chain: P
Molecule details ›
Chain: P
Length: 295 amino acids
Theoretical weight: 33.01 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6ZN18 (Residues: 209-503; Coverage: 57%)
Gene name: AEBP2
SUZ12 Chain: Z
Molecule details ›
Chain: Z
Length: 135 amino acids
Theoretical weight: 11.51 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
Protein Jumonji Chain: B
Molecule details ›
Chain: B
Length: 345 amino acids
Theoretical weight: 37.71 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q92833 (Residues: 106-450; Coverage: 28%)
Gene names: JARID2, JMJ

Ligands and Environments

No bound ligands
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-7334
Expression system: Trichoplusia ni

Quick links

Citations

38 review citations

Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes.
Barbour et al. (2020)
37 more

20 mentions without citation

Molecular Mechanisms Directing PRC2 Recruitment and H3K27 Methylation.
Laugesen et al. (2019)
19 more