› 4yyd

X-ray diffraction
1.52Å resolution

Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide

Released:
DOI: 10.2210/pdb4yyd/pdb
PDB 4yyd coloured by chain and viewed from the front.
PDB 4yyd coloured by chain and viewed from the side.
PDB 4yyd coloured by chain and viewed from the top.
Source organism: Homo sapiens
Primary publication:
A Subset of Human Bromodomains Recognizes Butyryllysine and Crotonyllysine Histone Peptide Modifications.
Flynn EM, Huang OW, Poy F, Oppikofer M, Bellon SF, Tang Y, Cochran AG
Structure (2015)
PMID: 26365797

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Bromodomain-containing protein 9 Chain: A
Molecule details ›
Chain: A
Length: 108 amino acids
Theoretical weight: 12.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H8M2 (Residues: 134-239; Coverage: 18%)
Gene names: BRD9, UNQ3040/PRO9856
Sequence domains: Bromodomain
Structure domains: Bromodomain-like
Histone H4 Chain: Z
Molecule details ›
Chain: Z
Length: 11 amino acids
Theoretical weight: 1.11 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62805 (Residues: 2-12; Coverage: 11%)
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

No bound ligands
1 modified residue:
Ligand KCR 2 x KCR

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G
Spacegroup: C2221
Unit cell:
a: 35.437Å b: 71.021Å c: 102.373Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.199 0.226
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

32 review citations

An Expanding Repertoire of Protein Acylations.
Xu et al. (2022)
31 more