› 4y3o

X-ray diffraction
2.2Å resolution

Crystal structure of Ribosomal oxygenase NO66 in complex with substrate Rpl8 peptide and Ni(II) and cofactor N-oxalyglycine

Released:
DOI: 10.2210/pdb4y3o/pdb
PDB entry 4y3o coloured by chain, front view.
PDB entry 4y3o coloured by chain, side view.
PDB entry 4y3o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8.
Wang C, Zhang Q, Hang T, Tao Y, Ma X, Wu M, Zhang X, Zang J
Acta Crystallogr D Biol Crystallogr 71 1955-64 (2015)
PMID: 26327385

Function and Biology Details

Reaction catalysed: 
(1a) a [histone H3]-N(6),N(6)-dimethyl-L-lysine(36) + 2-oxoglutarate + O(2) = a [histone H3]-N(6)-methyl-L-lysine(36) + succinate + formaldehyde + CO(2)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158761 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ribosomal oxygenase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 466 amino acids
Theoretical weight: 52.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H6W3 (Residues: 176-641; Coverage: 73%)
Gene names: C14orf169, MAPJD, NO66, RIOX1
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL2 Chains: C, D
Molecule details ›
Chains: C, D
Length: 11 amino acids
Theoretical weight: 1.1 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62917 (Residues: 212-222; Coverage: 4%)
Gene name: RPL8

Ligands and Environments

4 bound ligands:
Ligand NI 2 x NI
Ligand OGA 2 x OGA
Ligand GOL 3 x GOL
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2
Unit cell:
a: 88.5Å b: 202.93Å c: 85.68Å
α: 90° β: 118.94° γ: 90°
R-values:
R R work R free
0.206 0.203 0.262
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Vitamin C-Sources, Physiological Role, Kinetics, Deficiency, Use, Toxicity, and Determination.
Doseděl et al. (2021)
3 more

2 mentions without citation

Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8.
Wang et al. (2015)
1 more