› 3id5

X-ray diffraction
4.01Å resolution

Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA

Released:
DOI: 10.2210/pdb3id5/pdb
PDB entry 3id5 coloured by chain, front view.
PDB entry 3id5 coloured by chain, side view.
PDB entry 3id5 coloured by chain, top view.
Source organism: Saccharolobus solfataricus
Primary publication:
Structural organization of box C/D RNA-guided RNA methyltransferase.
Ye K, Jia R, Lin J, Ju M, Peng J, Xu A, Zhang L
Proc Natl Acad Sci U S A 106 13808-13 (2009)
PMID: 19666563

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-157328 (preferred)
Entry contents:
3 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (4 distinct):
Nop domain-containing protein Chains: A, E
Molecule details ›
Chains: A, E
Length: 388 amino acids
Theoretical weight: 44.17 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97ZH3 (Residues: 1-380; Coverage: 92%)
Gene name: SSO0939
Sequence domains:
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase Chains: B, F
Molecule details ›
Chains: B, F
Length: 232 amino acids
Theoretical weight: 26.44 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: P58032 (Residues: 1-232; Coverage: 100%)
Gene names: C33_014, SSO0940, flpA
Sequence domains: Fibrillarin
Large ribosomal subunit protein eL8 Chains: C, G
Molecule details ›
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.08 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: P55858 (Residues: 1-127; Coverage: 100%)
Gene names: C04_031, SSO0091, rpl7ae
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
half C/D RNA Chains: D, H
Molecule details ›
Chains: D, H
Length: 35 nucleotides
Theoretical weight: 11.26 KDa

Ligands and Environments

1 bound ligand:
Ligand SAM 2 x SAM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P41212
Unit cell:
a: 265.485Å b: 265.485Å c: 129.434Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.286 0.285 0.304
Expression system: Escherichia coli

Quick links

Citations

13 review citations

The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA.
Watkins et al. (2012)
12 more

5 mentions without citation

Structural organization of box C/D RNA-guided RNA methyltransferase.
Ye et al. (2009)
4 more