› 5xfq

X-ray diffraction
2.4Å resolution

Ternary complex of PHF1, a DNA duplex and a histone peptide

Released:
DOI: 10.2210/pdb5xfq/pdb
PDB entry 5xfq coloured by chain, front view.
PDB entry 5xfq coloured by chain, side view.
PDB entry 5xfq coloured by chain, top view.
Source organisms:
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-119389 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
PHD finger protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 336 amino acids
Theoretical weight: 37.63 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Z1B8 (Residues: 25-360; Coverage: 60%)
Gene names: Phf1, Plc1, Tctex-3, Tctex3
Sequence domains:
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Histone H3.1 Chains: E, F
Molecule details ›
Chains: E, F
Length: 13 amino acids
Theoretical weight: 1.43 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 30-42; Coverage: 10%)
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: C, D
Molecule details ›
Chains: C, D
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: C2
Unit cell:
a: 141.243Å b: 62.55Å c: 97.338Å
α: 90° β: 103.04° γ: 90°
R-values:
R R work R free
0.224 0.222 0.258
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

60 review citations

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

5 mentions without citation

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