› 6f57

X-ray diffraction
3.1Å resolution

Crystal structure of DNMT3A-DNMT3L in complex with single CpG-containing DNA

Released:
DOI: 10.2210/pdb6f57/pdb
PDB entry 6f57 coloured by chain, front view.
PDB entry 6f57 coloured by chain, side view.
PDB entry 6f57 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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119877 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA (cytosine-5)-methyltransferase 3A Chains: A, D
Molecule details ›
Chains: A, D
Length: 285 amino acids
Theoretical weight: 32.72 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
DNA (5'-D(*AP*GP*AP*GP*CP*GP*CP*AP*TP*G)-3') Chains: E, G
Molecule details ›
Chains: E, G
Length: 10 nucleotides
Theoretical weight: 3.09 KDa
DNA (5'-D(*CP*AP*TP*GP*ZP*GP*CP*TP*CP*T)-3') Chains: F, H
Molecule details ›
Chains: F, H
Length: 11 nucleotides
Theoretical weight: 3.27 KDa

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
No bound ligands
1 modified residue:
Ligand Z 2 x Z

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P21212
Unit cell:
a: 176.611Å b: 49.559Å c: 162.259Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.211 0.242
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

39 review citations

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

6 mentions without citation

Structural basis for DNMT3A-mediated de novo DNA methylation.
Zhang et al. (2018)
5 more