› 5gh9

X-ray diffraction
1.45Å resolution

Crystal structure of CBP Bromodomain with H3K56ac peptide

Released:
DOI: 10.2210/pdb5gh9/pdb
PDB entry 5gh9 coloured by chain, front view.
PDB entry 5gh9 coloured by chain, side view.
PDB entry 5gh9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insight into the recognition of acetylated histone H3K56ac mediated by the bromodomain of CREB-binding protein.
Xu L, Cheng A, Huang M, Zhang J, Jiang Y, Wang C, Li F, Bao H, Gao J, Wang N, Liu J, Wu J, Wong CCL, Ruan K
FEBS J 284 3422-3436 (2017)
PMID: 28815970

Function and Biology Details

Reaction catalysed: 
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159432 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
CREB-binding protein Chain: A
Molecule details ›
Chain: A
Length: 118 amino acids
Theoretical weight: 14.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q92793 (Residues: 1081-1196; Coverage: 5%)
Gene names: CBP, CREBBP
Sequence domains: Bromodomain
Structure domains: Bromodomain-like
Histone H3.1 Chain: B
Molecule details ›
Chain: B
Length: 14 amino acids
Theoretical weight: 1.72 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 45-58; Coverage: 10%)
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

No bound ligands
1 modified residue:
Ligand ALY 1 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 42.826Å b: 45.832Å c: 66.038Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.147 0.145 0.176
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

6 citation in other articles

TRIM66 reads unmodified H3R2K4 and H3K56ac to respond to DNA damage in embryonic stem cells.
Chen et al. (2019)
5 more

2 mentions without citation

Structural insight into the recognition of acetylated histone H3K56ac mediated by the bromodomain of CREB-binding protein.
Xu et al. (2017)
1 more