6kda

X-ray diffraction
2.91Å resolution

Crystal structure of human DNMT3B-DNMT3L in complex with DNA containing CpGpG site

Released:
Source organism: Homo sapiens

Function and Biology Details

Reaction catalysed:
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-120135 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
DNA (cytosine-5)-methyltransferase 3B Chains: A, D
Molecule details ›
Chains: A, D
Length: 286 amino acids
Theoretical weight: 32.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBC3 (Residues: 571-853; Coverage: 33%)
Gene name: DNMT3B
Sequence domains: C-5 cytosine-specific DNA methylase
DNA (cytosine-5)-methyltransferase 3-like Chains: B, C
Molecule details ›
Chains: B, C
Length: 204 amino acids
Theoretical weight: 23.63 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UJW3 (Residues: 178-379; Coverage: 52%)
Gene name: DNMT3L
DNA (25-MER) Chains: E, F
Molecule details ›
Chains: E, F
Length: 25 nucleotides
Theoretical weight: 7.7 KDa

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE TPS 05A
Spacegroup: P31
Unit cell:
a: 193.872Å b: 193.872Å c: 49.741Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.189 0.188 0.22
Expression system: Escherichia coli