› 7v0e

X-ray diffraction
3.27Å resolution

Crystal structure of the macro-oligomeric form of DNMT3B methyltransferase domain.

Released:
DOI: 10.2210/pdb7v0e/pdb
PDB entry 7v0e coloured by chain, front view.
PDB entry 7v0e coloured by chain, side view.
PDB entry 7v0e coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of DNMT3B homo-oligomer reveals vulnerability to impairment by ICF mutations.
Gao L, Guo Y, Biswal M, Lu J, Yin J, Fang J, Chen X, Shao Z, Huang M, Wang Y, Wang GG, Song J
Nat Commun 13 4249 (2022)
PMID: 35869095

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:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193646 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA (cytosine-5)-methyltransferase 3B Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 285 amino acids
Theoretical weight: 32.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UBC3 (Residues: 569-853; Coverage: 33%)
Gene name: DNMT3B
Sequence domains: C-5 cytosine-specific DNA methylase

Ligands and Environments


Cofactor: Ligand SAH 8 x SAH
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P32
Unit cell:
a: 164.393Å b: 164.393Å c: 209.175Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.206 0.206 0.235
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Epigenetic Targets in Schizophrenia Development and Therapy.
Wawrzczak-Bargieła et al. (2023)
3 other articles

1 mention without citation

Structural basis for the allosteric regulation and dynamic assembly of DNMT3B.
Lu et al. (2023)