› 5ye4

X-ray diffraction
1.8Å resolution

Crystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment

Released:
DOI: 10.2210/pdb5ye4/pdb
PDB entry 5ye4 coloured by chain, front view.
PDB entry 5ye4 coloured by chain, side view.
PDB entry 5ye4 coloured by chain, top view.
Source organisms:
Primary publication:
JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.
Handoko L, Kaczkowski B, Hon CC, Lizio M, Wakamori M, Matsuda T, Ito T, Jeyamohan P, Sato Y, Sakamoto K, Yokoyama S, Kimura H, Minoda A, Umehara T
Epigenetics 13 410-431 (2018)
PMID: 30080437

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-211484 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
1A9D7 VH CH1 chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 211 amino acids
Theoretical weight: 22.63 KDa
Source organism: Mus musculus
Expression system: Mus musculus
1A9D7 L chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 213 amino acids
Theoretical weight: 23.75 KDa
Source organism: Mus musculus
Expression system: Mus musculus
Structure domains: Immunoglobulins
Histone H4 Chains: E, F
Molecule details ›
Chains: E, F
Length: 12 amino acids
Theoretical weight: 1.19 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62805 (Residues: 2-13; Coverage: 12%)
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

Ligands and Environments

1 bound ligand:
Ligand ZN 26 x ZN
1 modified residue:
Ligand ALY 4 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P21
Unit cell:
a: 39.346Å b: 164.093Å c: 73.7Å
α: 90° β: 104.5° γ: 90°
R-values:
R R work R free
0.194 0.194 0.224
Expression systems:
  • Mus musculus
  • Not provided

Quick links

Citations

3 review citations

Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials.
Cheng et al. (2019)
2 more

1 mention without citation

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.
Handoko et al. (2018)