› 3mqk

X-ray diffraction
2.8Å resolution

Cbf5-Nop10-Gar1 complex binding with 17mer RNA containing ACA trinucleotide

Released:
DOI: 10.2210/pdb3mqk/pdb
PDB entry 3mqk coloured by chain, front view.
PDB entry 3mqk coloured by chain, side view.
PDB entry 3mqk coloured by chain, top view.
Source organism: Pyrococcus furiosus
Primary publication:
Structural and functional evidence of high specificity of Cbf5 for ACA trinucleotide.
Zhou J, Liang B, Li H
RNA 17 244-50 (2011)
PMID: 21149572

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)
PDBe Complex ID:
PDB-CPX-181663 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (5 distinct):
Probable tRNA pseudouridine synthase B Chain: A
Molecule details ›
Chain: A
Length: 328 amino acids
Theoretical weight: 37.12 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7LWY0 (Residues: 8-335; Coverage: 97%)
Gene names: PF1785, truB
Sequence domains:
Structure domains:
Ribosome biogenesis protein Nop10 Chain: B
Molecule details ›
Chain: B
Length: 52 amino acids
Theoretical weight: 6.21 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U1R4 (Residues: 4-55; Coverage: 87%)
Gene names: PF1141, nop10
Sequence domains: Nucleolar RNA-binding protein, Nop10p family
Structure domains: H/ACA ribonucleoprotein complex, subunit Nop10
Small nucleolar rnp gar1-like protein Chain: C
Molecule details ›
Chain: C
Length: 75 amino acids
Theoretical weight: 8.67 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U029 (Residues: 8-82; Coverage: 72%)
Gene name: PF1791
Sequence domains: Gar1/Naf1 RNA binding region
Structure domains: Probable tRNA pseudouridine synthase domain
RNA (5'-R(P*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 13 nucleotides
Theoretical weight: 4.12 KDa
RNA (5'-R(P*CP*GP*AP*UP*CP*CP*AP*CP*A)-3') Chain: E
Molecule details ›
Chain: E
Length: 9 nucleotides
Theoretical weight: 2.81 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: P6522
Unit cell:
a: 105.696Å b: 105.696Å c: 243.925Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.19 0.185 0.244
Expression system: Escherichia coli

Quick links

Citations

3 review citations

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

2 mentions without citation

Structural and functional evidence of high specificity of Cbf5 for ACA trinucleotide.
Zhou et al. (2011)
1 more