› 5vdc

X-ray diffraction
1.6Å resolution

Crystal structure of the human DPF2 tandem PHD finger domain

Released:
DOI: 10.2210/pdb5vdc/pdb
PDB entry 5vdc coloured by chain, front view.
PDB entry 5vdc coloured by chain, side view.
PDB entry 5vdc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Histone-binding of DPF2 mediates its repressive role in myeloid differentiation.
Huber FM, Greenblatt SM, Davenport AM, Martinez C, Xu Y, Vu LP, Nimer SD, Hoelz A
Proc Natl Acad Sci U S A 114 6016-6021 (2017)
PMID: 28533407

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-187749 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Zinc finger protein ubi-d4 Chain: A
Molecule details ›
Chain: A
Length: 126 amino acids
Theoretical weight: 14.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q92785 (Residues: 270-391; Coverage: 31%)
Gene names: BAF45D, DPF2, REQ, UBID4
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand GOL 2 x GOL
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: I422
Unit cell:
a: 107.5Å b: 107.5Å c: 53.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.143 0.141 0.191
Expression system: Escherichia coli

Quick links

Citations

4 review citations

The language of chromatin modification in human cancers.
Zhao et al. (2021)
3 more

3 mentions without citation

Conserved Structure and Evolution of DPF Domain of PHF10-The Specific Subunit of PBAF Chromatin Remodeling Complex.
Chugunov et al. (2021)
2 more