› 3o7b

X-ray diffraction
1.45Å resolution

Crystal structure of Archaeoglobus Fulgidus Nep1 bound to S-adenosylhomocysteine

Released:
DOI: 10.2210/pdb3o7b/pdb
PDB entry 3o7b coloured by chain, front view.
PDB entry 3o7b coloured by chain, side view.
PDB entry 3o7b coloured by chain, top view.
Source organism: Archaeoglobus fulgidus
Primary publication:
Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.
Thomas SR, Keller CA, Szyk A, Cannon JR, Laronde-Leblanc NA
Nucleic Acids Res 39 2445-57 (2011)
PMID: 21087996

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128140 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosomal RNA small subunit methyltransferase Nep1 Chain: A
Molecule details ›
Chain: A
Length: 244 amino acids
Theoretical weight: 28.38 KDa
Source organism: Archaeoglobus fulgidus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: O29524 (Residues: 1-219; Coverage: 100%)
Gene names: AF_0734, nep1
Sequence domains: EMG1/NEP1 methyltransferase
Structure domains: Alpha/beta knot

Ligands and Environments

2 bound ligands:
Ligand TYR 1 x TYR
Ligand SAH 1 x SAH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P3121
Unit cell:
a: 70.083Å b: 70.083Å c: 95.19Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.199 0.198 0.211
Expression system: Escherichia coli BL21

Quick links

Citations

10 review citations

'View From A Bridge': A New Perspective on Eukaryotic rRNA Base Modification.
Sharma et al. (2015)
9 more

3 mentions without citation

Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.
Thomas et al. (2011)
2 more