› 5ciu

X-ray diffraction
2.24Å resolution

Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain

Released:
DOI: 10.2210/pdb5ciu/pdb
PDB entry 5ciu coloured by chain, front view.
PDB entry 5ciu coloured by chain, side view.
PDB entry 5ciu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B.
Rondelet G, Dal Maso T, Willems L, Wouters J
J Struct Biol 194 357-67 (2016)
PMID: 26993463

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180743 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
DNA (cytosine-5)-methyltransferase 3B Chains: A, B
Molecule details ›
Chains: A, B
Length: 150 amino acids
Theoretical weight: 16.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UBC3 (Residues: 206-355; Coverage: 18%)
Gene name: DNMT3B
Sequence domains: PWWP domain
Structure domains:
Histone H3.2 Chains: C, D
Molecule details ›
Chains: C, D
Length: 15 amino acids
Theoretical weight: 1.67 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q71DI3 (Residues: 29-43; Coverage: 11%)
Gene names: H3C13, H3C14, H3C15, H3F2, H3FM, HIST2H3A, HIST2H3C, HIST2H3D

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
1 modified residue:
Ligand M3L 2 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 2
Spacegroup: P3221
Unit cell:
a: 73.437Å b: 73.437Å c: 158.2Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.227 0.224 0.259
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

20 review citations

DNA methylation and DNA methyltransferases.
Edwards et al. (2017)
19 more

7 mentions without citation

Structural Basis of DNMT1 and DNMT3A-Mediated DNA Methylation.
Ren et al. (2018)
6 more