› 7w5p

X-ray diffraction
2.3Å resolution

Crystal Structure of the dioxygenase CcTet from Coprinopsis cinereain bound to 12bp N6-methyldeoxyadenine (6mA) containing duplex DNA

Released:
DOI: 10.2210/pdb7w5p/pdb
PDB entry 7w5p coloured by chain, front view.
PDB entry 7w5p coloured by chain, side view.
PDB entry 7w5p coloured by chain, top view.
Source organisms:
Primary publication:
A fungal dioxygenase CcTet serves as a eukaryotic 6mA demethylase on duplex DNA.
Mu Y, Zhang L, Hu J, Zhou J, Lin HW, He C, Chen HZ, Zhang L
Nat Chem Biol 18 733-741 (2022)
PMID: 35654845

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-108767 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
2OGFeDO JBP1/TET oxygenase domain-containing protein Chains: A, D, G, H
Molecule details ›
Chains: A, D, G, H
Length: 430 amino acids
Theoretical weight: 48.12 KDa
Source organism: Coprinopsis cinerea
Expression system: Escherichia coli
UniProt:
  • Canonical: A8P1J0 (Residues: 1-430; Coverage: 100%)
Gene name: CC1G_05589
Sequence domains: Oxygenase domain of the 2OGFeDO superfamily
DNA (12-MER) Chains: B, E
Molecule details ›
Chains: B, E
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA Chains: C, F
Molecule details ›
Chains: C, F
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MN 4 x MN
Ligand OGA 4 x OGA
1 modified residue:
Ligand 6MA 2 x 6MA

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 104.788Å b: 105.198Å c: 196.717Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.228 0.257
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Mammalian DNA N6-methyladenosine: Challenges and new insights.
Feng et al. (2023)
1 more