› 4npl

X-ray diffraction
1.65Å resolution

Crystal structure of Zebrafish ALKBH5 in complex with alpha-ketoglutarate

Released:
DOI: 10.2210/pdb4npl/pdb
PDB entry 4npl coloured by chain, front view.
PDB entry 4npl coloured by chain, side view.
PDB entry 4npl coloured by chain, top view.
Source organism: Danio rerio
Primary publication:
Crystal structure of the RNA demethylase ALKBH5 from zebrafish.
Chen W, Zhang L, Zheng G, Fu Y, Ji Q, Liu F, Chen H, He C
FEBS Lett 588 892-8 (2014)
PMID: 24561204

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170724 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA demethylase ALKBH5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 250 amino acids
Theoretical weight: 28.36 KDa
Source organism: Danio rerio
Expression system: Escherichia coli
UniProt:
  • Canonical: Q08BA6 (Residues: 38-287; Coverage: 71%)
Gene name: alkbh5
Sequence domains: 2OG-Fe(II) oxygenase superfamily
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like

Ligands and Environments

2 bound ligands:
Ligand MN 2 x MN
Ligand AKG 2 x AKG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 65.948Å b: 68.595Å c: 114.909Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.209 0.238
Expression system: Escherichia coli

Quick links

Citations

22 review citations

Gene expression regulation mediated through reversible m⁶A RNA methylation.
Fu et al. (2014)
21 more

3 mentions without citation

Structural Insights into N6-methyladenosine (m6A) Modification in the Transcriptome.
Huang et al. (2018)
2 more