› 5i3l

X-ray diffraction
1.85Å resolution

DPF3b in complex with H3K14ac peptide

Released:
DOI: 10.2210/pdb5i3l/pdb
PDB entry 5i3l coloured by chain, front view.
PDB entry 5i3l coloured by chain, side view.
PDB entry 5i3l coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of DPF3b in complex with an acetylated histone peptide.
Li W, Zhao A, Tempel W, Loppnau P, Liu Y
J Struct Biol 195 365-372 (2016)
PMID: 27402533

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159431 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Zinc finger protein DPF3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 115 amino acids
Theoretical weight: 12.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q92784 (Residues: 254-368; Coverage: 30%)
Gene names: BAF45C, CERD4, DPF3
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Histone H3.1 Chain: C
Molecule details ›
Chain: C
Length: 21 amino acids
Theoretical weight: 2.23 KDa
Source organism: synthetic construct
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-21; Coverage: 15%)
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 8 x ZN
Ligand EDO 1 x EDO
Ligand UNX 32 x UNX
Ligand NA 1 x NA
1 modified residue:
Ligand ALY 1 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2221
Unit cell:
a: 99.822Å b: 121.641Å c: 56.446Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.182 0.212
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

2 review citations

Studying Chromatin Epigenetics with Fluorescence Microscopy.
Stepanov et al. (2022)
1 more

5 mentions without citation

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