6w8b

X-ray diffraction
2.4Å resolution

Structure of DNMT3A in complex with CGA DNA

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-120815 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
DNA (cytosine-5)-methyltransferase 3A Chains: A, D, H, K
Molecule details ›
Chains: A, D, H, K
Length: 285 amino acids
Theoretical weight: 32.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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, I, J
Molecule details ›
Chains: B, C, I, J
Length: 209 amino acids
Theoretical weight: 24.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UJW3 (Residues: 178-386; Coverage: 54%)
Gene name: DNMT3L
CGA DNA (25-MER) Chains: E, F, L, M
Molecule details ›
Chains: E, F, L, M
Length: 25 nucleotides
Theoretical weight: 7.7 KDa

Ligands and Environments


Cofactor: Ligand SAH 4 x SAH
No bound ligands
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P32
Unit cell:
a: 186.347Å b: 186.347Å c: 81.671Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.212 0.212 0.233
Expression system: Escherichia coli