› 5xfr

X-ray diffraction
2.25Å resolution

Ternary complex of MTF2, DNA and histone

Released:
DOI: 10.2210/pdb5xfr/pdb
PDB entry 5xfr coloured by chain, front view.
PDB entry 5xfr coloured by chain, side view.
PDB entry 5xfr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Polycomb-like proteins link the PRC2 complex to CpG islands.
Li H, Liefke R, Jiang J, Kurland JV, Tian W, Deng P, Zhang W, He Q, Patel DJ, Bulyk ML, Shi Y, Wang Z
Nature 549 287-291 (2017)
PMID: 28869966

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119390 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
Metal-response element-binding transcription factor 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 317 amino acids
Theoretical weight: 36.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y483 (Residues: 43-358; Coverage: 53%)
Gene names: MTF2, PCL2
Sequence domains:
Histone H3.1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 8 amino acids
Theoretical weight: 924 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 34-41; Coverage: 6%)
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
DNA (5'-D(*GP*GP*GP*CP*GP*GP*CP*CP*GP*CP*CP*CP*T)-3') Chains: E, F
Molecule details ›
Chains: E, F
Length: 13 nucleotides
Theoretical weight: 3.97 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
1 modified residue:
Ligand M3L 2 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P3121
Unit cell:
a: 137.743Å b: 137.743Å c: 101.226Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.204 0.203 0.231
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

61 review citations

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

6 mentions without citation

Engaging chromatin: PRC2 structure meets function.
Chammas et al. (2020)
5 more