6pa7

Electron Microscopy
2.94Å resolution

The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome.

Released:

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:

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 135 amino acids
Theoretical weight: 15.3 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 2-136; Coverage: 99%)
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: C, G
Molecule details ›
Chains: C, G
Length: 129 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P06897 (Residues: 2-130; Coverage: 99%)
Sequence domains:
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 123 amino acids
Theoretical weight: 13.66 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 5-126; Coverage: 97%)
DNA (cytosine-5)-methyltransferase 3A Chains: K, P
Molecule details ›
Chains: K, P
Length: 689 amino acids
Theoretical weight: 77.91 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9Y6K1 (Residues: 224-912; Coverage: 76%)
Gene name: DNMT3A
Sequence domains:
DNA (cytosine-5)-methyltransferase 3B Chains: N, S
Molecule details ›
Chains: N, S
Length: 770 amino acids
Theoretical weight: 86.29 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9UBC3 (Residues: 1-853; Coverage: 90%)
  • Best match: Q9UBC3-3 (Residues: 1-770)
Gene name: DNMT3B
Sequence domains:
DNA (167-MER) Chain: I
Molecule details ›
Chain: I
Length: 167 nucleotides
Theoretical weight: 51.33 KDa
DNA (167-MER) Chain: J
Molecule details ›
Chain: J
Length: 167 nucleotides
Theoretical weight: 51.79 KDa

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.94Å
Relevant EMDB volumes: EMD-20281
Expression systems:
  • Escherichia coli
  • Spodoptera frugiperda