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

X-ray diffraction
2.27Å resolution
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:
Assembly composition:
hetero dimer (preferred)
Entry contents: 4 distinct polypeptide molecules

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Assemblies

Assembly 1
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Assembly Name: Histone H3.1 and Polycomb Protein EED
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Multimeric state: hetero dimer
Accessible surface area: 22230.31 Å2
Buried surface area: 1043.16 Å2
Dissociation area: 521.58 Å2
Dissociation energy (ΔGdiss): -0.36 kcal/mol
Dissociation entropy (TΔSdiss): 6.9 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-219065
Assembly 2 (preferred)
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Assembly Name: SET domain-containing protein and Polycomb protein VEFS-Box domain-containing protein
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Multimeric state: hetero dimer
Accessible surface area: 46042.26 Å2
Buried surface area: 1575.25 Å2
Dissociation area: 0 Å2
Dissociation energy (ΔGdiss): 0 kcal/mol
Dissociation entropy (TΔSdiss): 0 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-219064

Macromolecules

putative polycomb protein EED
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
Pfam: WD domain, G-beta repeat
InterPro:
putative polycomb protein EED in PDB entry 5m5g, assembly 1, front view.
putative polycomb protein EED in PDB entry 5m5g, assembly 1, side view.
putative polycomb protein EED in PDB entry 5m5g, assembly 1, top view.
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SET domain-containing protein
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
Pfam:
InterPro:
SET domain-containing protein in PDB entry 5m5g, assembly 2, front view.
SET domain-containing protein in PDB entry 5m5g, assembly 2, side view.
SET domain-containing protein in PDB entry 5m5g, assembly 2, top view.
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Histone H3.1
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
Histone H3.1 in PDB entry 5m5g, assembly 1, front view.
Histone H3.1 in PDB entry 5m5g, assembly 1, side view.
Histone H3.1 in PDB entry 5m5g, assembly 1, top view.
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Polycomb protein VEFS-Box domain-containing protein
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
Polycomb protein VEFS-Box domain-containing protein in PDB entry 5m5g, assembly 2, front view.
Polycomb protein VEFS-Box domain-containing protein in PDB entry 5m5g, assembly 2, side view.
Polycomb protein VEFS-Box domain-containing protein in PDB entry 5m5g, assembly 2, top view.
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