› 5deu

X-ray diffraction
1.8Å resolution

Crystal structure of TET2-5hmC complex

Released:
DOI: 10.2210/pdb5deu/pdb
PDB entry 5deu coloured by chain, front view.
PDB entry 5deu coloured by chain, side view.
PDB entry 5deu 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-118560 (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, 1844-1935; Coverage: 22%)
Gene names: KIAA1546, Nbla00191, TET2
Sequence domains: Oxygenase domain of the 2OGFeDO superfamily
DNA (5'-D(*AP*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
DNA (5'-D(P*CP*CP*AP*CP*(5HC)P*GP*GP*TP*GP*GP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 11 nucleotides
Theoretical weight: 3.38 KDa

Ligands and Environments

5 bound ligands:
Ligand OGA 1 x OGA
Ligand MES 1 x MES
Ligand FE 1 x FE
Ligand ZN 3 x ZN
Ligand CL 1 x CL
1 modified residue:
Ligand 5HC 2 x 5HC

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2221
Unit cell:
a: 48.262Å b: 87.522Å c: 260.864Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.177 0.212
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

8 mentions without citation

Acetylation- and Methylation-Related Epigenetic Proteins in the Context of Their Targets.
Javaid et al. (2017)
7 more