› 5y1z

X-ray diffraction
2.68Å resolution

Crystal structure of ZMYND8 PHD-BROMO-PWWP tandem in complex with Drebrin ADF-H domain

Released:
DOI: 10.2210/pdb5y1z/pdb
PDB entry 5y1z coloured by chain, front view.
PDB entry 5y1z coloured by chain, side view.
PDB entry 5y1z coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The Structure of the ZMYND8/Drebrin Complex Suggests a Cytoplasmic Sequestering Mechanism of ZMYND8 by Drebrin.
Yao N, Li J, Liu H, Wan J, Liu W, Zhang M
Structure 25 1657-1666.e3 (2017)
PMID: 28966017

Function and Biology Details

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-172537 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Drebrin Chains: A, B
Molecule details ›
Chains: A, B
Length: 137 amino acids
Theoretical weight: 14.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q16643 (Residues: 1-135; Coverage: 21%)
Gene names: D0S117E, DBN1
Sequence domains: Cofilin/tropomyosin-type actin-binding protein
Structure domains: Severin
MYND-type zinc finger-containing chromatin reader ZMYND8 Chains: C, D
Molecule details ›
Chains: C, D
Length: 324 amino acids
Theoretical weight: 37.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9ULU4 (Residues: 83-406; Coverage: 27%)
Gene names: KIAA1125, PRKCBP1, RACK7, ZMYND8
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 6 x SO4
Ligand ZN 6 x ZN
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P212121
Unit cell:
a: 54.183Å b: 138.095Å c: 161.164Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.181 0.178 0.234
Expression system: Escherichia coli

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Citations

1 review citation

Bromodomain biology and drug discovery.
Zaware et al. (2019)
4 other articles