5yx2

X-ray diffraction
2.65Å resolution

Crystal structure of DNMT3A-DNMT3L in complex with DNA containing two CpG sites

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:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
DNA (cytosine-5)-methyltransferase 3A Chains: A, D
Molecule details ›
Chains: A, D
Length: 285 amino acids
Theoretical weight: 32.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y6K1 (Residues: 628-912; Coverage: 31%)
Gene name: DNMT3A
Sequence domains: C-5 cytosine-specific DNA methylase
DNA (cytosine-5)-methyltransferase 3-like Chains: B, C
Molecule details ›
Chains: B, C
Length: 208 amino acids
Theoretical weight: 24.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UJW3 (Residues: 178-385; Coverage: 54%)
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
1 bound ligand:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: R3
Unit cell:
a: 205.424Å b: 205.424Å c: 89.337Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.192 0.191 0.222
Expression system: Escherichia coli BL21(DE3)