› 3a1b

X-ray diffraction
2.29Å resolution

Crystal structure of the DNMT3A ADD domain in complex with histone H3

Released:
DOI: 10.2210/pdb3a1b/pdb
PDB entry 3a1b coloured by chain, front view.
PDB entry 3a1b coloured by chain, side view.
PDB entry 3a1b coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain.
Otani J, Nankumo T, Arita K, Inamoto S, Ariyoshi M, Shirakawa M
EMBO Rep 10 1235-41 (2009)
PMID: 19834512

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:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159398 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA (cytosine-5)-methyltransferase 3A; Histone H3.1 Chain: A
Molecule details ›
Chain: A
Length: 159 amino acids
Theoretical weight: 18.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P68431 (Residues: 2-21; Coverage: 15%)
  • Canonical: Q9Y6K1 (Residues: 476-614; Coverage: 15%)
Gene names: DNMT3A, H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand EDO 7 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P41212
Unit cell:
a: 68.547Å b: 68.547Å c: 109.95Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.192 0.224
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

90 review citations

Establishing, maintaining and modifying DNA methylation patterns in plants and animals.
Law et al. (2010)
89 more

14 mentions without citation

Perceiving the epigenetic landscape through histone readers.
Musselman et al. (2012)
13 more