› 6axj

X-ray diffraction
2.38Å resolution

Crystal structure of the Yaf9 YEATS domain bound to H3K27ac

Released:
DOI: 10.2210/pdb6axj/pdb
PDB entry 6axj coloured by chain, front view.
PDB entry 6axj coloured by chain, side view.
PDB entry 6axj coloured by chain, top view.
Source organisms:
Primary publication:
Yaf9 subunit of the NuA4 and SWR1 complexes targets histone H3K27ac through its YEATS domain.
Klein BJ, Ahmad S, Vann KR, Andrews FH, Mayo ZA, Bourriquen G, Bridgers JB, Zhang J, Strahl BD, Côté J, Kutateladze TG
Nucleic Acids Res 46 421-430 (2018)
PMID: 29145630

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero hexamer (preferred)
hetero dodecamer
Assembly name:
PDBe Complex ID:
PDB-CPX-156907 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein AF-9 homolog Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 169 amino acids
Theoretical weight: 19.36 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P53930 (Residues: 8-171; Coverage: 73%)
Gene names: N1966, YAF9, YNL107W
Sequence domains: YEATS family
Structure domains: YEATS domain
Histone H3.1 Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 11 amino acids
Theoretical weight: 1.12 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 22-32; Coverage: 8%)
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

2 bound ligands:
Ligand SO4 4 x SO4
Ligand GOL 10 x GOL
1 modified residue:
Ligand ALY 4 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: R3
Unit cell:
a: 140.318Å b: 140.318Å c: 129.054Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.181 0.179 0.227
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Old cogs, new tricks: the evolution of gene expression in a chromatin context.
Talbert et al. (2019)
6 more

1 mention without citation

Yaf9 subunit of the NuA4 and SWR1 complexes targets histone H3K27ac through its YEATS domain.
Klein et al. (2018)