› 6brr

X-ray diffraction
2.97Å resolution

Crystal structure of DNMT3A (R836A)-DNMT3L in complex with DNA containing two CpG sites

Released:
DOI: 10.2210/pdb6brr/pdb
PDB entry 6brr coloured by chain, front view.
PDB entry 6brr coloured by chain, side view.
PDB entry 6brr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for DNMT3A-mediated de novo DNA methylation.
Zhang ZM, Lu R, Wang P, Yu Y, Chen D, Gao L, Liu S, Ji D, Rothbart SB, Wang Y, Wang GG, Song J
Nature 554 387-391 (2018)
PMID: 29414941

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-119623 (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: 32.63 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: 209 amino acids
Theoretical weight: 24.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UJW3 (Residues: 178-386; Coverage: 54%)
Gene name: DNMT3L
Structure domains: Vaccinia Virus protein VP39
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
No bound ligands
1 modified residue:
Ligand PYO 2 x PYO

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: R3
Unit cell:
a: 205.005Å b: 205.005Å c: 89.358Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.202 0.199 0.242
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

38 review citations

Fates of CD8+ T cells in Tumor Microenvironment.
Maimela et al. (2019)
37 more

5 mentions without citation

Regulation of DNA Methylation by Cannabidiol and Its Implications for Psychiatry: New Insights from In Vivo and In Silico Models.
Domingos et al. (2022)
4 more