› 5xfp

X-ray diffraction
2.3Å resolution

Binary complex of PHF1 and a double stranded DNA

Released:
DOI: 10.2210/pdb5xfp/pdb
PDB entry 5xfp coloured by chain, front view.
PDB entry 5xfp coloured by chain, side view.
PDB entry 5xfp 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

Assemblies composition:
monomeric
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119388 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
PHD finger protein 1 Chains: A, B, E
Molecule details ›
Chains: A, B, E
Length: 336 amino acids
Theoretical weight: 37.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O43189 (Residues: 25-360; Coverage: 59%)
Gene names: PCL1, PHF1
Sequence domains:
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
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
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 12 x ZN
Ligand TRS 2 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P212121
Unit cell:
a: 109.601Å b: 110.291Å c: 118.853Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.209 0.244
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

64 review citations

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

1 mention without citation

Polycomb-like proteins link the PRC2 complex to CpG islands.
Li et al. (2017)