› 3oin

X-ray diffraction
1.9Å resolution

Crystal structure of Saccharomyces cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA

Released:
DOI: 10.2210/pdb3oin/pdb
PDB entry 3oin coloured by chain, front view.
PDB entry 3oin coloured by chain, side view.
PDB entry 3oin coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
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

Reaction catalysed: 
S-adenosyl-L-methionine + pseudouridine(1191) in yeast 18S rRNA = S-adenosyl-L-homocysteine + N(1)-methylpseudouridine(1191) in yeast 18S rRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170327 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Ribosomal RNA small subunit methyltransferase NEP1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 253 amino acids
Theoretical weight: 28.04 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q06287 (Residues: 1-252; Coverage: 100%)
Gene names: EMG1, L9470.5, NEP1, YLR186W
Sequence domains: EMG1/NEP1 methyltransferase
Structure domains: Alpha/beta knot
5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*AP*CP*GP*CP*CP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.44 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
3 bound ligands:
Ligand GOL 2 x GOL
Ligand MG 1 x MG
Ligand CL 1 x CL
1 modified residue:
Ligand SCY 2 x SCY

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 44.774Å b: 88.749Å c: 115.751Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.192 0.23
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

10 review citations

Ribosome assembly coming into focus.
Klinge et al. (2019)
9 more

5 mentions without citation

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