› 3kqi

X-ray diffraction
1.78Å resolution

crystal structure of PHF2 PHD domain complexed with H3K4Me3 peptide

Released:
DOI: 10.2210/pdb3kqi/pdb
PDB entry 3kqi coloured by chain, front view.
PDB entry 3kqi coloured by chain, side view.
PDB entry 3kqi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation.
Wen H, Li J, Song T, Lu M, Kan PY, Lee MG, Sha B, Shi X
J Biol Chem 285 9322-9326 (2010)
PMID: 20129925

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-130854 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Lysine-specific demethylase PHF2 Chain: A
Molecule details ›
Chain: A
Length: 75 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O75151 (Residues: 1-70; Coverage: 6%)
Gene names: CENP-35, KIAA0662, PHF2
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Histone H3.1 Chain: B
Molecule details ›
Chain: B
Length: 12 amino acids
Theoretical weight: 1.35 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-13; Coverage: 9%)
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

Ligands and Environments

4 bound ligands:
Ligand ZN 2 x ZN
Ligand GOL 1 x GOL
Ligand CL 1 x CL
Ligand MG 2 x MG
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P6522
Unit cell:
a: 77.757Å b: 77.758Å c: 72.116Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.191 0.19 0.218
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

36 review citations

Histone demethylases in development and disease.
Pedersen et al. (2010)
35 more

9 mentions without citation

The PHD finger: a versatile epigenome reader.
Sanchez et al. (2011)
8 more