› 4ccm

X-ray diffraction
2.51Å resolution

60S ribosomal protein L8 histidine hydroxylase (NO66) in complex with Mn(II), N-oxalylglycine (NOG) and 60S ribosomal protein L8 (RPL8 G220C) peptide fragment (complex-1)

Released:
DOI: 10.2210/pdb4ccm/pdb
PDB entry 4ccm coloured by chain, front view.
PDB entry 4ccm coloured by chain, side view.
PDB entry 4ccm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Ribosomal oxygenases are structurally conserved from prokaryotes to humans.
Chowdhury R, Sekirnik R, Brissett NC, Krojer T, Ho CH, Ng SS, Clifton IJ, Ge W, Kershaw NJ, Fox GC, Muniz JRC, Vollmar M, Phillips C, Pilka ES, Kavanagh KL, von Delft F, Oppermann U, McDonough MA, Doherty AJ, Schofield CJ
OpenAccess logo Nature 510 422-426 (2014)
PMID: 24814345

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 octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-549119 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ribosomal oxygenase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 467 amino acids
Theoretical weight: 53.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9H6W3 (Residues: 183-641; Coverage: 72%)
Gene names: C14orf169, MAPJD, NO66, RIOX1
Sequence domains:
Structure domains:
Large ribosomal subunit protein uL2 Chains: C, D
Molecule details ›
Chains: C, D
Length: 35 amino acids
Theoretical weight: 3.74 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62917 (Residues: 205-239; Coverage: 14%)
Gene name: RPL8

Ligands and Environments

3 bound ligands:
Ligand MN 2 x MN
Ligand OGA 2 x OGA
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: C2
Unit cell:
a: 154.77Å b: 83.5Å c: 96.87Å
α: 90° β: 100.2° γ: 90°
R-values:
R R work R free
0.228 0.228 0.236
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

23 review citations

2-Oxoglutarate-Dependent Oxygenases.
Islam et al. (2018)
22 more

2 mentions without citation

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