› 7wl0

X-ray diffraction
2.5Å resolution

Crystal structure of human ALKBH5 in complex with N-oxalylglycine (NOG) and m6A-containing ssRNA

Released:
DOI: 10.2210/pdb7wl0/pdb
PDB entry 7wl0 coloured by chain, front view.
PDB entry 7wl0 coloured by chain, side view.
PDB entry 7wl0 coloured by chain, top view.
Source organisms:
Primary publication:
Mechanisms of substrate recognition and N6-methyladenosine demethylation revealed by crystal structures of ALKBH5-RNA complexes.
Kaur S, Tam NY, McDonough MA, Schofield CJ, Aik WS
Nucleic Acids Res 50 4148-4160 (2022)
PMID: 35333330

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:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180130 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
RNA demethylase ALKBH5 Chains: A, C, E, G, I
Molecule details ›
Chains: A, C, E, G, I
Length: 220 amino acids
Theoretical weight: 25.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6P6C2 (Residues: 74-292; Coverage: 56%)
Gene names: ABH5, ALKBH5, OFOXD1
Sequence domains: 2OG-Fe(II) oxygenase superfamily
RNA (5'-R(*UP*GP*GP*(6MZ)P*CP*UP*GP*C)-3') Chains: B, D, F, H, J
Molecule details ›
Chains: B, D, F, H, J
Length: 8 nucleotides
Theoretical weight: 2.56 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MN 5 x MN
Ligand OGA 5 x OGA
Ligand FMT 1 x FMT
1 modified residue:
Ligand 6MZ 5 x 6MZ

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P21
Unit cell:
a: 59.77Å b: 132.37Å c: 77.96Å
α: 90° β: 100.99° γ: 90°
R-values:
R R work R free
0.198 0.196 0.24
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Interconnections between m6A RNA modification, RNA structure, and protein-RNA complex assembly.
Höfler et al. (2024)
4 more

1 mention without citation

Mechanisms of substrate recognition and N6-methyladenosine demethylation revealed by crystal structures of ALKBH5-RNA complexes.
Kaur et al. (2022)