› 5d9y

X-ray diffraction
1.97Å resolution

Crystal structure of TET2-5fC complex

Released:
DOI: 10.2210/pdb5d9y/pdb
PDB entry 5d9y coloured by chain, front view.
PDB entry 5d9y coloured by chain, side view.
PDB entry 5d9y coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insight into substrate preference for TET-mediated oxidation.
Hu L, Lu J, Cheng J, Rao Q, Li Z, Hou H, Lou Z, Zhang L, Li W, Gong W, Liu M, Sun C, Yin X, Li J, Tan X, Wang P, Wang Y, Fang D, Cui Q, Yang P, He C, Jiang H, Luo C, Xu Y
Nature 527 118-22 (2015)
PMID: 26524525

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-118548 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Methylcytosine dioxygenase TET2 Chain: A
Molecule details ›
Chain: A
Length: 462 amino acids
Theoretical weight: 51.4 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
DNA (5'-D(*AP*CP*TP*GP*TP*(5FC)P*GP*AP*AP*GP*CP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
DNA (5'-D(*AP*GP*CP*TP*TP*CP*GP*AP*CP*AP*GP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.66 KDa

Ligands and Environments

3 bound ligands:
Ligand OGA 1 x OGA
Ligand FE 1 x FE
Ligand ZN 3 x ZN
1 modified residue:
Ligand 5FC 1 x 5FC

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2221
Unit cell:
a: 48.154Å b: 87.958Å c: 268.02Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.205 0.248
Expression system: Escherichia coli

Quick links

Citations

55 review citations

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

4 mentions without citation

Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families.
Berger et al. (2021)
3 more