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Solution NMR

Solution structure of the double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone H4 peptide containing acetylation at Lysine 16

Released:
DOI: 10.2210/pdb2kwn/pdb
PDB 2kwn coloured by chain and viewed from the front.
PDB 2kwn coloured by chain and viewed from the side.
PDB 2kwn coloured by chain and viewed from the top.
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
OpenAccess logo 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)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone H4 Chain: B
Molecule details ›
Chain: B
Length: 15 amino acids
Theoretical weight: 1.68 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62805 (Residues: 10-24; Coverage: 15%)
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, 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
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Refinement method: DGSA-distance geometry simulated annealing, torsion angle dynamics
Chemical shifts: BMR16861  
Expression systems:
  • Not provided
  • Escherichia coli BL21

Quick links

Citations

62 review citations

Exploring the Histone Acetylation Cycle in the Protozoan Model Tetrahymena thermophila.
Wahab et al. (2020)
61 more

3 mentions without citation

Combinatorial readout of dual histone modifications by paired chromatin-associated modules.
Wang et al. (2011)
2 more