› 2kwo

Solution NMR

Solution structure of the double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone H4 peptide containing N-terminal acetylation at Serine 1

Released:
DOI: 10.2210/pdb2kwo/pdb
PDB entry 2kwo coloured by chain, ensemble of 20 models, front view.
PDB entry 2kwo coloured by chain, ensemble of 20 models, side view.
PDB entry 2kwo coloured by chain, ensemble of 20 models, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b.
Zeng L, Zhang Q, Li S, Plotnikov AN, Walsh MJ, Zhou MM
Nature 466 258-62 (2010)
PMID: 20613843

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-158684 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone H4 Chain: B
Molecule details ›
Chain: B
Length: 20 amino acids
Theoretical weight: 2.04 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62805 (Residues: 2-21; Coverage: 19%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Zinc finger protein DPF3 Chain: A
Molecule details ›
Chain: A
Length: 114 amino acids
Theoretical weight: 12.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q92784 (Residues: 261-372; Coverage: 30%)
Gene names: BAF45C, CERD4, DPF3
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
1 modified residue:
Ligand SAC 1 x SAC

Experiments and Validation Details

Entry percentile scores
Refinement method: DGSA-distance geometry simulated annealing, torsion angle dynamics
Expression systems:
  • Not provided
  • Escherichia coli BL21

Quick links

Citations

73 review citations

Regulation of chromatin by histone modifications.
Bannister et al. (2011)
72 more

7 mentions without citation

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