› 3dm1

X-ray diffraction
2.4Å resolution

Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide

Released:
DOI: 10.2210/pdb3dm1/pdb
PDB entry 3dm1 coloured by chain, front view.
PDB entry 3dm1 coloured by chain, side view.
PDB entry 3dm1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of the chromodomain of Cbx3 bound to methylated peptides from histone h1 and G9a.
Ruan J, Ouyang H, Amaya MF, Ravichandran M, Loppnau P, Min J, Zang J
PLoS One 7 e35376 (2012)
PMID: 22514736

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-L-lysine(9) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(9)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero octamer
Assembly name:
PDBe Complex ID:
PDB-CPX-171585 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Chromobox protein homolog 3 Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 58 amino acids
Theoretical weight: 6.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13185 (Residues: 29-86; Coverage: 32%)
Gene name: CBX3
Sequence domains: Chromo (CHRromatin Organisation MOdifier) domain
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Histone-lysine N-methyltransferase EHMT2 Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 12 amino acids
Theoretical weight: 1.49 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q96KQ7 (Residues: 179-190; Coverage: 1%)
Gene names: BAT8, C6orf30, EHMT2, G9A, KMT1C, NG36

Ligands and Environments

No bound ligands
1 modified residue:
Ligand M3L 4 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ DW
Spacegroup: P3221
Unit cell:
a: 83.671Å b: 83.671Å c: 110.288Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.222 0.22 0.267
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

The functional diversity of protein lysine methylation.
Lanouette et al. (2014)
4 more

7 mentions without citation

Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives.
Andreoli et al. (2013)
6 more