› 4nrm

X-ray diffraction
2.17Å resolution

Crystal structure of human ALKBH5 in complex with citrate and acetate

Released:
DOI: 10.2210/pdb4nrm/pdb
PDB 4nrm coloured by chain and viewed from the front.
PDB 4nrm coloured by chain and viewed from the side.
PDB 4nrm coloured by chain and viewed from the top.
Source organism: Homo sapiens
Primary publication:
Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition.
Feng C, Liu Y, Wang G, Deng Z, Zhang Q, Wu W, Tong Y, Cheng C, Chen Z
J Biol Chem 289 11571-11583 (2014)
PMID: 24616105

Function and Biology Details

Reaction catalysed: 
N(6)-methyladenosine in mRNA + 2-oxoglutarate + O(2) = adenosine in mRNA + formaldehyde + succinate + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA demethylase ALKBH5 Chain: A
Molecule details ›
Chain: A
Length: 230 amino acids
Theoretical weight: 26.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6P6C2 (Residues: 66-292; Coverage: 58%)
Gene names: ABH5, ALKBH5, OFOXD1
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like

Ligands and Environments

2 bound ligands:
Ligand FLC 1 x FLC
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P43212
Unit cell:
a: 56.726Å b: 56.726Å c: 146.315Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.203 0.232
Expression system: Escherichia coli

Quick links

Citations

21 review citations

Multi-substrate selectivity based on key loops and non-homologous domains: new insight into ALKBH family.
Xu et al. (2021)
20 more

3 mentions without citation

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