› 5szc

X-ray diffraction
1.19Å resolution

Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with monomethylated K4 and acetylated K14

Released:
DOI: 10.2210/pdb5szc/pdb
PDB entry 5szc coloured by chain, front view.
PDB entry 5szc coloured by chain, side view.
PDB entry 5szc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification of H3K4me1-associated proteins at mammalian enhancers.
Local A, Huang H, Albuquerque CP, Singh N, Lee AY, Wang W, Wang C, Hsia JE, Shiau AK, Ge K, Corbett KD, Wang D, Zhou H, Ren B
Nat Genet 50 73-82 (2018)
PMID: 29255264

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159430 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Zinc finger protein DPF3 Chain: A
Molecule details ›
Chain: A
Length: 115 amino acids
Theoretical weight: 12.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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: H
Molecule details ›
Chain: H
Length: 18 amino acids
Theoretical weight: 2 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-19; Coverage: 13%)
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

2 bound ligands:
Ligand ZN 4 x ZN
Ligand MPD 1 x MPD
2 modified residues:
Ligand MLZ 1 x MLZ
Ligand ALY 1 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P43212
Unit cell:
a: 39.321Å b: 39.321Å c: 147.571Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.149 0.147 0.167
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

32 review citations

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation.
Catarino et al. (2018)
31 more

4 mentions without citation

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