› 5zmd

X-ray diffraction
3.3Å resolution

Crystal structure of FTO in complex with m6dA modified ssDNA

Released:
DOI: 10.2210/pdb5zmd/pdb
PDB entry 5zmd coloured by chain, front view.
PDB entry 5zmd coloured by chain, side view.
PDB entry 5zmd coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into FTO's catalytic mechanism for the demethylation of multiple RNA substrates.
Zhang X, Wei LH, Wang Y, Xiao Y, Liu J, Zhang W, Yan N, Amu G, Tang X, Zhang L, Jia G
Proc Natl Acad Sci U S A 116 2919-2924 (2019)
PMID: 30718435

Function and Biology Details

Reaction catalysed: 
N(6)-methyladenosine in mRNA + 2-oxoglutarate + O(2) = adenosine in mRNA + formaldehyde + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119522 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Alpha-ketoglutarate-dependent dioxygenase FTO Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 463 amino acids
Theoretical weight: 53.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9C0B1 (Residues: 37-499; Coverage: 92%)
Gene names: FTO, KIAA1752
Sequence domains:
Structure domains:
DNA (5'-D(P*TP*CP*TP*(6MA)P*TP*AP*TP*CP*G)-3') Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 9 nucleotides
Theoretical weight: 2.72 KDa
Source organism: DNA launch vector pDE-GFP2
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 4 x 6MA

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: I212121
Unit cell:
a: 122.736Å b: 160.033Å c: 276.756Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.272 0.271 0.292
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

55 review citations

Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers.
Shi et al. (2019)
54 more

12 mentions without citation

Targeting the RNA demethylase FTO for cancer therapy.
Zhou et al. (2021)
11 more