› 2rfk

X-ray diffraction
2.87Å resolution

Substrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein Complex

Released:
DOI: 10.2210/pdb2rfk/pdb
PDB entry 2rfk coloured by chain, front view.
PDB entry 2rfk coloured by chain, side view.
PDB entry 2rfk coloured by chain, top view.
Source organism: Pyrococcus furiosus
Primary publication:
Substrate RNA positioning in the archaeal H/ACA ribonucleoprotein complex.
Liang B, Xue S, Terns RM, Terns MP, Li H
Nat Struct Mol Biol 14 1189-95 (2007)
PMID: 18059286

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-181662 (preferred)
Entry contents:
3 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (6 distinct):
Probable tRNA pseudouridine synthase B Chain: A
Molecule details ›
Chain: A
Length: 334 amino acids
Theoretical weight: 37.86 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7LWY0 (Residues: 5-338; Coverage: 98%)
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
Small nucleolar rnp gar1-like protein Chain: C
Molecule details ›
Chain: C
Length: 74 amino acids
Theoretical weight: 8.52 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U029 (Residues: 8-81; Coverage: 71%)
Gene name: PF1791
Sequence domains: Gar1/Naf1 RNA binding region
Structure domains: Probable tRNA pseudouridine synthase domain
guide RNA 1 Chain: D
Molecule details ›
Chain: D
Length: 21 nucleotides
Theoretical weight: 6.8 KDa
guide RNA 2 Chain: E
Molecule details ›
Chain: E
Length: 26 nucleotides
Theoretical weight: 8.23 KDa
target RNA Chain: F
Molecule details ›
Chain: F
Length: 14 nucleotides
Theoretical weight: 4.54 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P41212
Unit cell:
a: 96.561Å b: 96.561Å c: 240.978Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.25 0.248 0.3
Expression system: Escherichia coli

Quick links

Citations

12 review citations

Box H/ACA small ribonucleoproteins.
Kiss et al. (2010)
11 more

10 mentions without citation

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