› 5m5g

X-ray diffraction
2.27Å resolution

Crystal structure of the Chaetomium Thermophilum polycomb repressive complex 2 (PRC2)

Released:
DOI: 10.2210/pdb5m5g/pdb
PDB entry 5m5g coloured by chain, front view.
PDB entry 5m5g coloured by chain, side view.
PDB entry 5m5g coloured by chain, top view.
Source organisms:
Primary publication:
Comment on "Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2".
Zhang Y, Justin N, Wilson JR, Gamblin SJ
Science 354 1543 (2016)
PMID: 28008037

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-219064 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
putative polycomb protein EED Chain: A
Molecule details ›
Chain: A
Length: 605 amino acids
Theoretical weight: 66.02 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: G0S8H7 (Residues: 1-565; Coverage: 100%)
Gene name: CTHT_0029920
Sequence domains: WD domain, G-beta repeat
SET domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 937 amino acids
Theoretical weight: 106.87 KDa
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: G0SDW4 (Residues: 191-952; Coverage: 50%)
Gene name: CTHT_0053230
Sequence domains:
Histone H3.1 Chain: D
Molecule details ›
Chain: D
Length: 11 amino acids
Theoretical weight: 1.15 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 23-33; Coverage: 8%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J
Polycomb protein VEFS-Box domain-containing protein Chain: E
Molecule details ›
Chain: E
Length: 9 amino acids
Theoretical weight: 926 Da
Source organism: Thermochaetoides thermophila DSM 1495
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: G0RYC6 (Residues: 531-539; Coverage: 1%)
Gene name: CTHT_0006210

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand SAH 1 x SAH
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2, APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 81.554Å b: 74.612Å c: 128.508Å
α: 90° β: 107.7° γ: 90°
R-values:
R R work R free
0.173 0.171 0.221
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

2 review citations

Structure, mechanism, and regulation of polycomb-repressive complex 2.
Moritz et al. (2018)
1 more