› 3hay

X-ray diffraction
4.99Å resolution

Crystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus

Released:
DOI: 10.2210/pdb3hay/pdb
PDB entry 3hay coloured by chain, front view.
PDB entry 3hay coloured by chain, side view.
PDB entry 3hay coloured by chain, top view.
Source organism: Pyrococcus furiosus
Primary publication:
Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase.
Duan J, Li L, Lu J, Wang W, Ye K
Mol Cell 34 427-39 (2009)
PMID: 19481523

Function and Biology Details

Reaction catalysed: 
tRNA uridine(55) = tRNA pseudouridine(55)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-181660 (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (6 distinct):
Probable tRNA pseudouridine synthase B Chain: A
Molecule details ›
Chain: A
Length: 346 amino acids
Theoretical weight: 39.45 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7LWY0 (Residues: 1-340; Coverage: 100%)
Gene names: PF1785, truB
Sequence domains:
Small nucleolar rnp gar1-like protein Chain: B
Molecule details ›
Chain: B
Length: 104 amino acids
Theoretical weight: 12.34 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U029 (Residues: 1-104; Coverage: 100%)
Gene name: PF1791
Sequence domains: Gar1/Naf1 RNA binding region
Ribosome biogenesis protein Nop10 Chain: C
Molecule details ›
Chain: C
Length: 60 amino acids
Theoretical weight: 7.21 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U1R4 (Residues: 1-60; Coverage: 100%)
Gene names: PF1141, nop10
Sequence domains: Nucleolar RNA-binding protein, Nop10p family
Large ribosomal subunit protein eL8 Chain: D
Molecule details ›
Chain: D
Length: 130 amino acids
Theoretical weight: 14.31 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U160 (Residues: 2-123; Coverage: 99%)
Gene names: PF1367, rpl7ae
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
H/ACA RNA Chain: E
Molecule details ›
Chain: E
Length: 71 nucleotides
Theoretical weight: 22.95 KDa
5'-R(*AP*UP*AP*AP*UP*UP*(FHU)P*GP*AP*CP*UP*CP*AP*A)-3' Chain: F
Molecule details ›
Chain: F
Length: 14 nucleotides
Theoretical weight: 4.45 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
1 modified residue:
Ligand FHU 1 x FHU

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P6422
Unit cell:
a: 189.518Å b: 189.518Å c: 279.045Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.325 0.323 0.367
Expression system: Escherichia coli

Quick links

Citations

25 review citations

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

16 mentions without citation

Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function.
Sloan et al. (2017)
15 more