› 2xl3

X-ray diffraction
2.7Å resolution

WDR5 IN COMPLEX WITH AN RBBP5 PEPTIDE AND HISTONE H3 PEPTIDE

Released:
DOI: 10.2210/pdb2xl3/pdb
PDB entry 2xl3 coloured by chain, front view.
PDB entry 2xl3 coloured by chain, side view.
PDB entry 2xl3 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Characterization of a novel WDR5-binding site that recruits RbBP5 through a conserved motif to enhance methylation of histone H3 lysine 4 by mixed lineage leukemia protein-1.
Odho Z, Southall SM, Wilson JR
J Biol Chem 285 32967-32976 (2010)
PMID: 20716525

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-158506 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
WD repeat-containing protein 5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 334 amino acids
Theoretical weight: 36.64 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P61965 (Residues: 1-334; Coverage: 100%)
Gene names: Big, Big3, Wdr5
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Retinoblastoma-binding protein 5 Chains: C, E
Molecule details ›
Chains: C, E
Length: 14 amino acids
Theoretical weight: 1.54 KDa
Source organism: Mus musculus
Expression system: Not provided
UniProt:
  • Canonical: Q8BX09 (Residues: 369-381; Coverage: 2%)
Gene name: Rbbp5
Histone H3.1 Chains: D, F
Molecule details ›
Chains: D, F
Length: 9 amino acids
Theoretical weight: 1.1 KDa
Source organism: Mus musculus
Expression system: Not provided
UniProt:
  • Canonical: P68433 (Residues: 2-9; Coverage: 6%)
Gene names: H3.1-221, H3.1-291, H3.1-I, H3a, H3c1, H3c10, H3c11, H3c8, H3g, H3h, H3i, Hist1h3a, Hist1h3g, Hist1h3h, Hist1h3i

Ligands and Environments

1 bound ligand:
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P21
Unit cell:
a: 47.1Å b: 81.32Å c: 86.35Å
α: 90° β: 91.13° γ: 90°
R-values:
R R work R free
0.179 0.176 0.235
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

19 review citations

SET for life: biochemical activities and biological functions of SET domain-containing proteins.
Herz et al. (2013)
18 more

2 mentions without citation

Characterization of a novel WDR5-binding site that recruits RbBP5 through a conserved motif to enhance methylation of histone H3 lysine 4 by mixed lineage leukemia protein-1.
Odho et al. (2010)
1 more