› 8ba5

X-ray diffraction
1.45Å resolution

Crystal structure of the DNMT3A ADD domain

Released:
DOI: 10.2210/pdb8ba5/pdb
PDB entry 8ba5 coloured by chain, front view.
PDB entry 8ba5 coloured by chain, side view.
PDB entry 8ba5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The MECP2-TRD domain interacts with the DNMT3A-ADD domain at the H3-tail binding site.
Kunert S, Linhard V, Weirich S, Choudalakis M, Osswald F, Krämer L, Köhler AR, Bröhm A, Wollenhaupt J, Schwalbe H, Jeltsch A
OpenAccess logo Protein Sci 32 e4542 (2023)
PMID: 36519786

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195368 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA (cytosine-5)-methyltransferase 3A Chain: A
Molecule details ›
Chain: A
Length: 144 amino acids
Theoretical weight: 16.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y6K1 (Residues: 476-614; Coverage: 15%)
Gene name: DNMT3A
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand EDO 2 x EDO
Ligand ZN 3 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P6122
Unit cell:
a: 57.8Å b: 57.8Å c: 138.56Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.187 0.213
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Unveiling the methyl transfer mechanisms in the epigenetic machinery DNMT3A-3 L: A comprehensive study integrating assembly dynamics with catalytic reactions.
Yang et al. (2023)

1 mention without citation

The MECP2-TRD domain interacts with the DNMT3A-ADD domain at the H3-tail binding site.
Kunert et al. (2023)