› 2xb1

X-ray diffraction
1.9Å resolution

Crystal structure of the human Pygo2 PHD finger in complex with the B9L HD1 domain

Released:
DOI: 10.2210/pdb2xb1/pdb
PDB entry 2xb1 coloured by chain, front view.
PDB entry 2xb1 coloured by chain, side view.
PDB entry 2xb1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Allosteric remodelling of the histone H3 binding pocket in the Pygo2 PHD finger triggered by its binding to the B9L/BCL9 co-factor.
Miller TC, Rutherford TJ, Johnson CM, Fiedler M, Bienz M
J Mol Biol 401 969-84 (2010)
PMID: 20637214

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183189 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
B-cell CLL/lymphoma 9-like protein; Pygopus homolog 2 Chains: A, C
Molecule details ›
Chains: A, C
Length: 105 amino acids
Theoretical weight: 11.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9BRQ0 (Residues: 325-387; Coverage: 16%)
  • Canonical: Q86UU0 (Residues: 224-271; Coverage: 3%)
Gene names: BCL9L, DLNB11, PP7910, PYGO2
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand GOL 2 x GOL
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P212121
Unit cell:
a: 38.75Å b: 69.73Å c: 82.07Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.171 0.217
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Readout of epigenetic modifications.
Patel et al. (2013)
9 more

4 mentions without citation

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