› 6w89

X-ray diffraction
2.5Å resolution

Structure of DNMT3A (R882H) in complex with CGA DNA

Released:
DOI: 10.2210/pdb6w89/pdb
PDB entry 6w89 coloured by chain, front view.
PDB entry 6w89 coloured by chain, side view.
PDB entry 6w89 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for impairment of DNA methylation by the DNMT3A R882H mutation.
Anteneh H, Fang J, Song J
Nat Commun 11 2294 (2020)
PMID: 32385248

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
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120814 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
DNA (cytosine-5)-methyltransferase 3A Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 285 amino acids
Theoretical weight: 32.7 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, H, I
Molecule details ›
Chains: B, C, H, I
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, K, L
Molecule details ›
Chains: E, F, K, L
Length: 25 nucleotides
Theoretical weight: 7.7 KDa

Ligands and Environments


Cofactor: Ligand SAH 4 x SAH
1 bound ligand:
Ligand CIT 4 x CIT
1 modified residue:
Ligand PYO 4 x PYO

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P32
Unit cell:
a: 187.559Å b: 187.559Å c: 82.398Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.197 0.196 0.24
Expression system: Escherichia coli

Quick links

Citations

9 review citations

The language of chromatin modification in human cancers.
Zhao et al. (2021)
8 more

1 mention without citation

Point Mutation Specific Antibodies in B-Cell and T-Cell Lymphomas and Leukemias: Targeting IDH2, KRAS, BRAF and Other Biomarkers RHOA, IRF8, MYD88, ID3, NRAS, SF3B1 and EZH2.
Singh et al. (2021)