› 4nm6

X-ray diffraction
2.03Å resolution

Crystal structure of TET2-DNA complex

Released:
DOI: 10.2210/pdb4nm6/pdb
PDB entry 4nm6 coloured by chain, front view.
PDB entry 4nm6 coloured by chain, side view.
PDB entry 4nm6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation.
Hu L, Li Z, Cheng J, Rao Q, Gong W, Liu M, Shi YG, Zhu J, Wang P, Xu Y
Cell 155 1545-55 (2013)
PMID: 24315485

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117883 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Methylcytosine dioxygenase TET2 Chain: A
Molecule details ›
Chain: A
Length: 463 amino acids
Theoretical weight: 51.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6N021 (Residues: 1129-1480, 1844-1936; Coverage: 22%)
Gene names: KIAA1546, Nbla00191, TET2
Sequence domains: Oxygenase domain of the 2OGFeDO superfamily
5'-D(*AP*CP*CP*AP*CP*(5CM)P*GP*GP*TP*GP*GP*T)-3' Chains: B, C
Molecule details ›
Chains: B, C
Length: 12 nucleotides
Theoretical weight: 3.68 KDa

Ligands and Environments

3 bound ligands:
Ligand ZN 3 x ZN
Ligand FE2 1 x FE2
Ligand OGA 1 x OGA
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2221
Unit cell:
a: 48.296Å b: 88.186Å c: 262.962Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.202 0.243
Expression system: Escherichia coli

Quick links

Citations

56 review citations

TET-mediated active DNA demethylation: mechanism, function and beyond.
Wu et al. (2017)
55 more

36 mentions without citation

Mechanism and function of oxidative reversal of DNA and RNA methylation.
Shen et al. (2014)
35 more