› 5exh

X-ray diffraction
1.3Å resolution

Crystal structure of mTET3-CXXC domain in complex with 5-carboxylcytosine DNA at 1.3 Angstroms resolution.

Released:
DOI: 10.2210/pdb5exh/pdb
PDB entry 5exh coloured by chain, front view.
PDB entry 5exh coloured by chain, side view.
PDB entry 5exh coloured by chain, top view.
Source organisms:
Primary publication:
Tet3 Reads 5-Carboxylcytosine through Its CXXC Domain and Is a Potential Guardian against Neurodegeneration.
Jin SG, Zhang ZM, Dunwell TL, Harter MR, Wu X, Johnson J, Li Z, Liu J, Szabó PE, Lu Q, Xu GL, Song J, Pfeifer GP
Cell Rep 14 493-505 (2016)
PMID: 26774490

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118652 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Methylcytosine dioxygenase TET3 Chain: C
Molecule details ›
Chain: C
Length: 47 amino acids
Theoretical weight: 5.5 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8BG87 (Residues: 51-96; Coverage: 3%)
Gene name: Tet3
DNA (5'-D(*GP*AP*AP*TP*CP*(1CC)P*GP*GP*AP*TP*TP*C)-3') Chains: A, B
Molecule details ›
Chains: A, B
Length: 12 nucleotides
Theoretical weight: 3.71 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
1 modified residue:
Ligand 1CC 2 x 1CC

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: C2
Unit cell:
a: 74.959Å b: 27.23Å c: 47.06Å
α: 90° β: 104.44° γ: 90°
R-values:
R R work R free
0.169 0.168 0.187
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

28 review citations

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

5 mentions without citation

Detecting and interpreting DNA methylation marks.
Ren et al. (2018)
4 more