› 2rfi

X-ray diffraction
1.59Å resolution

Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide

Released:
DOI: 10.2210/pdb2rfi/pdb
PDB entry 2rfi coloured by chain, front view.
PDB entry 2rfi coloured by chain, side view.
PDB entry 2rfi coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural biology of human H3K9 methyltransferases.
Wu H, Min J, Lunin VV, Antoshenko T, Dombrovski L, Zeng H, Allali-Hassani A, Campagna-Slater V, Vedadi M, Arrowsmith CH, Plotnikov AN, Schapira M
PLoS One 5 e8570 (2010)
PMID: 20084102

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

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-163221 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase EHMT1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 285 amino acids
Theoretical weight: 32.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H9B1 (Residues: 982-1266; Coverage: 22%)
Gene names: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D
Sequence domains:
Structure domains: SET domain
Histone H3 Chains: P, Q
Molecule details ›
Chains: P, Q
Length: 11 amino acids
Theoretical weight: 1.16 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand SAH 2 x SAH
1 modified residue:
Ligand MLY 2 x MLY

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 84.593Å b: 85.627Å c: 95.67Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.193 0.22
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

31 review citations

S-adenosyl-methionine-dependent methyltransferases: highly versatile enzymes in biocatalysis, biosynthesis and other biotechnological applications.
Struck et al. (2012)
30 more

25 mentions without citation

Histone lysine methylation dynamics: establishment, regulation, and biological impact.
Black et al. (2012)
24 more