› 4u7t

X-ray diffraction
2.9Å resolution

Crystal structure of DNMT3A-DNMT3L in complex with histone H3

Released:
DOI: 10.2210/pdb4u7t/pdb
PDB entry 4u7t coloured by chain, front view.
PDB entry 4u7t coloured by chain, side view.
PDB entry 4u7t coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insight into autoinhibition and histone H3-induced activation of DNMT3A.
Guo X, Wang L, Li J, Ding Z, Xiao J, Yin X, He S, Shi P, Dong L, Li G, Tian C, Wang J, Cong Y, Xu Y
Nature 517 640-4 (2015)
PMID: 25383530

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-160873 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
DNA (cytosine-5)-methyltransferase 3A Chains: A, C
Molecule details ›
Chains: A, C
Length: 445 amino acids
Theoretical weight: 50.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y6K1 (Residues: 476-912; Coverage: 48%)
Gene name: DNMT3A
Sequence domains:
DNA (cytosine-5)-methyltransferase 3-like Chains: B, D
Molecule details ›
Chains: B, D
Length: 209 amino acids
Theoretical weight: 24.12 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UJW3 (Residues: 178-379; Coverage: 52%)
Gene name: DNMT3L
Structure domains: Vaccinia Virus protein VP39
Histone H3.3 Chains: F, G
Molecule details ›
Chains: F, G
Length: 12 amino acids
Theoretical weight: 1.31 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P84243 (Residues: 2-13; Coverage: 9%)
Gene names: H3-3A, H3-3B, H3.3A, H3.3B, H3F3, H3F3A, H3F3B, PP781

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
1 bound ligand:
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P65
Unit cell:
a: 183.823Å b: 183.823Å c: 123.265Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.225 0.223 0.261
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

59 review citations

Role of TET enzymes in DNA methylation, development, and cancer.
Rasmussen et al. (2016)
58 more

16 mentions without citation

DNA methylation pathways and their crosstalk with histone methylation.
Du et al. (2015)
15 more