› 4lt5

X-ray diffraction
2.89Å resolution

Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA

Released:
DOI: 10.2210/pdb4lt5/pdb
PDB entry 4lt5 coloured by chain, front view.
PDB entry 4lt5 coloured by chain, side view.
PDB entry 4lt5 coloured by chain, top view.
Source organism: Naegleria gruberi
Primary publication:
Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA.
Hashimoto H, Pais JE, Zhang X, Saleh L, Fu ZQ, Dai N, Corrêa IR, Zheng Y, Cheng X
Nature 506 391-5 (2014)
PMID: 24390346

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112421 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Tet-like dioxygenase 1 Chain: A
Molecule details ›
Chain: A
Length: 327 amino acids
Theoretical weight: 37.37 KDa
Source organism: Naegleria gruberi
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D2W6T1 (Residues: 2-321; Coverage: 100%)
Gene names: NAEGRDRAFT_55029, TET1
Structure domains: Double-stranded beta-helix
DNA Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.29 KDa
Source organism: Naegleria gruberi
Expression system: Not provided
DNA Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.29 KDa
Source organism: Naegleria gruberi
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MN 1 x MN
Ligand EDO 9 x EDO
Ligand SO4 4 x SO4
Ligand OGA 1 x OGA
1 modified residue:
Ligand 5CM 2 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM, APS BEAMLINE 22-ID
Spacegroup: I212121
Unit cell:
a: 83.954Å b: 108.648Å c: 166.384Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.193 0.215
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

22 review citations

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

6 mentions without citation

The Mechanisms of Generation, Recognition, and Erasure of DNA 5-Methylcytosine and Thymine Oxidations.
Hashimoto et al. (2015)
5 more