› 4up0

X-ray diffraction
1.28Å resolution

Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and a H3K4me2 peptide

Released:
DOI: 10.2210/pdb4up0/pdb
PDB entry 4up0 coloured by chain, front view.
PDB entry 4up0 coloured by chain, side view.
PDB entry 4up0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Competitive binding of a benzimidazole to the histone-binding pocket of the Pygo PHD finger.
Miller TC, Rutherford TJ, Birchall K, Chugh J, Fiedler M, Bienz M
ACS Chem Biol 9 2864-74 (2014)
PMID: 25323450

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)
Assembly name:
PDBe Complex ID:
PDB-CPX-159418 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
B-cell CLL/lymphoma 9-like protein; Pygopus homolog 2 Chain: A
Molecule details ›
Chain: A
Length: 99 amino acids
Theoretical weight: 10.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BRQ0 (Residues: 327-387; Coverage: 15%)
  • Canonical: Q86UU0 (Residues: 240-268; Coverage: 2%)
Gene names: BCL9L, DLNB11, PP7910, PYGO2
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Histone H3.1 Chain: F
Molecule details ›
Chain: F
Length: 15 amino acids
Theoretical weight: 1.63 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-16; Coverage: 11%)
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

1 bound ligand:
Ligand ZN 2 x ZN
2 modified residues:
Ligand MLY 1 x MLY
Ligand ALY 1 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P41212
Unit cell:
a: 53.91Å b: 53.91Å c: 57.94Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.139 0.138 0.166
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

17 review citations

The WNT/β-catenin dependent transcription: A tissue-specific business.
Söderholm et al. (2021)
16 more

1 mention without citation

Competitive binding of a benzimidazole to the histone-binding pocket of the Pygo PHD finger.
Miller et al. (2014)