› 2vpg

X-ray diffraction
1.6Å resolution

Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex

Released:
DOI: 10.2210/pdb2vpg/pdb
PDB entry 2vpg coloured by chain, front view.
PDB entry 2vpg coloured by chain, side view.
PDB entry 2vpg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex.
Fiedler M, Sánchez-Barrena MJ, Nekrasov M, Mieszczanek J, Rybin V, Müller J, Evans P, Bienz M
Mol Cell 30 507-18 (2008)
PMID: 18498752

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-126329 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Pygopus homolog 1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 63 amino acids
Theoretical weight: 6.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y3Y4 (Residues: 340-398; Coverage: 14%)
Gene name: PYGO1
Sequence domains: PHD-finger
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
B-cell CLL/lymphoma 9 protein Chains: B, D
Molecule details ›
Chains: B, D
Length: 32 amino acids
Theoretical weight: 3.44 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O00512 (Residues: 176-205; Coverage: 2%)
Gene name: BCL9
Histone H3.1 Chains: P, R
Molecule details ›
Chains: P, R
Length: 18 amino acids
Theoretical weight: 2 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-19; Coverage: 13%)
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 GOL 1 x GOL
Ligand ZN 4 x ZN
2 modified residues:
Ligand DA2 2 x DA2
Ligand MLY 2 x MLY

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P4212
Unit cell:
a: 105.75Å b: 105.75Å c: 51.42Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.201 0.218
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

39 review citations

Wnt/beta-catenin signaling: components, mechanisms, and diseases.
MacDonald et al. (2009)
38 more

2 mentions without citation

The structural biology of canonical Wnt signalling.
Agostino et al. (2020)
1 more