› 4tmp

X-ray diffraction
2.3Å resolution

Crystal structure of AF9 YEATS bound to H3K9ac peptide

Released:
DOI: 10.2210/pdb4tmp/pdb
PDB entry 4tmp coloured by chain, front view.
PDB entry 4tmp coloured by chain, side view.
PDB entry 4tmp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
AF9 YEATS domain links histone acetylation to DOT1L-mediated H3K79 methylation.
Li Y, Wen H, Xi Y, Tanaka K, Wang H, Peng D, Ren Y, Jin Q, Dent SY, Li W, Li H, Shi X
Cell 159 558-71 (2014)
PMID: 25417107

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154674 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein AF-9 Chains: A, C
Molecule details ›
Chains: A, C
Length: 141 amino acids
Theoretical weight: 16.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P42568 (Residues: 1-138; Coverage: 24%)
Gene names: AF9, MLLT3, YEATS3
Sequence domains: YEATS family
Structure domains: YEATS domain
Histone H3.3 Chains: B, D
Molecule details ›
Chains: B, D
Length: 11 amino acids
Theoretical weight: 1.29 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P84243 (Residues: 2-12; Coverage: 8%)
Gene names: H3-3A, H3-3B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781

Ligands and Environments

1 bound ligand:
Ligand EDO 4 x EDO
1 modified residue:
Ligand ALY 2 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2221
Unit cell:
a: 42.537Å b: 195.704Å c: 106.675Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.162 0.229
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

67 review citations

50 years of protein acetylation: from gene regulation to epigenetics, metabolism and beyond.
Verdin et al. (2015)
66 more

24 mentions without citation

Metabolic regulation of gene expression through histone acylations.
Sabari et al. (2017)
23 more