› 3hjy

X-ray diffraction
3.65Å resolution

Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA

Released:
DOI: 10.2210/pdb3hjy/pdb
PDB entry 3hjy coloured by chain, front view.
PDB entry 3hjy coloured by chain, side view.
PDB entry 3hjy coloured by chain, top view.
Source organism: Pyrococcus furiosus
Primary publication:
Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA.
Liang B, Zhou J, Kahen E, Terns RM, Terns MP, Li H
Nat Struct Mol Biol 16 740-6 (2009)
PMID: 19478803

Function and Biology Details

Reaction catalysed: 
tRNA uridine(55) = tRNA pseudouridine(55)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181671 (preferred)
Entry contents:
2 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (5 distinct):
Probable tRNA pseudouridine synthase B Chain: A
Molecule details ›
Chain: A
Length: 327 amino acids
Theoretical weight: 36.99 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7LWY0 (Residues: 8-334; Coverage: 96%)
Gene names: PF1785, truB
Sequence domains:
Structure domains:
Ribosome biogenesis protein Nop10 Chain: B
Molecule details ›
Chain: B
Length: 53 amino acids
Theoretical weight: 6.35 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U1R4 (Residues: 3-55; Coverage: 88%)
Gene names: PF1141, nop10
Sequence domains: Nucleolar RNA-binding protein, Nop10p family
Structure domains: H/ACA ribonucleoprotein complex, subunit Nop10
5'-R(*GP*GP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*CP*CP*GP*CP*GP*GP*CP*GP*C)-3' Chain: C
Molecule details ›
Chain: C
Length: 21 nucleotides
Theoretical weight: 6.8 KDa
RNA (25-MER) Chain: D
Molecule details ›
Chain: D
Length: 25 nucleotides
Theoretical weight: 7.9 KDa
5'-R(*GP*GP*AP*GP*CP*GP*UP*GP*CP*GP*GP*UP*UP*U)-3' Chain: E
Molecule details ›
Chain: E
Length: 14 nucleotides
Theoretical weight: 4.54 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P6222
Unit cell:
a: 238.341Å b: 238.341Å c: 127.369Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.277 0.276 0.306
Expression system: Escherichia coli

Quick links

Citations

15 review citations

Ribosome biogenesis in the yeast Saccharomyces cerevisiae.
Woolford et al. (2013)
14 more

6 mentions without citation

The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification.
Hamma et al. (2010)
5 more