PDBe 2hvy

X-ray diffraction
2.3Å resolution

Crystal structure of an H/ACA box RNP from Pyrococcus furiosus

Released:
Source organism: Pyrococcus furiosus
Primary publication:
Crystal structure of an H/ACA box ribonucleoprotein particle.
Nature 443 302-7 (2006)
PMID: 16943774

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Entry contents:
4 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (5 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:
Structure 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
Structure domains: Probable tRNA pseudouridine synthase domain
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
Structure domains: H/ACA ribonucleoprotein complex, subunit Nop10
50S ribosomal protein L7Ae 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: 1-123; Coverage: 100%)
Gene names: PF1367, rpl7ae
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Structure domains: 60s Ribosomal Protein L30; Chain: A;
H/ACA RNA Chain: E
Molecule details ›
Chain: E
Length: 65 nucleotides
Theoretical weight: 21.02 KDa

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 83.031Å b: 90.95Å c: 114.064Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.24 0.238 0.278
Expression system: Escherichia coli