› 3pla

X-ray diffraction
3.15Å resolution

Crystal structure of a catalytically active substrate-bound box C/D RNP from Sulfolobus solfataricus

Released:
DOI: 10.2210/pdb3pla/pdb
PDB entry 3pla coloured by chain, front view.
PDB entry 3pla coloured by chain, side view.
PDB entry 3pla coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for site-specific ribose methylation by box C/D RNA protein complexes.
Lin J, Lai S, Jia R, Xu A, Zhang L, Lu J, Ye K
Nature 469 559-63 (2011)
PMID: 21270896

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-111993 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (5 distinct):
Nop domain-containing protein Chains: A, B, K
Molecule details ›
Chains: A, B, K
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:
Structure domains:
Large ribosomal subunit protein eL8 Chains: C, D, L
Molecule details ›
Chains: C, D, L
Length: 130 amino acids
Theoretical weight: 14.08 KDa
Source organism: Saccharolobus solfataricus 98/2
Expression system: Escherichia coli
UniProt:
  • Canonical: D0KRE2 (Residues: 1-130; Coverage: 100%)
Gene names: Ssol_1068, rpl7ae
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Structure domains: 60s Ribosomal Protein L30; Chain: A;
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase Chains: E, F, M
Molecule details ›
Chains: E, F, M
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
Structure domains:
C/D guide RNA Chains: G, H, N
Molecule details ›
Chains: G, H, N
Length: 40 nucleotides
Theoretical weight: 12.85 KDa
RNA (5'-R(*CP*CP*AP*UP*GP*AP*GP*UP*GP*U)-3') Chains: I, J, O
Molecule details ›
Chains: I, J, O
Length: 10 nucleotides
Theoretical weight: 3.18 KDa

Ligands and Environments

1 bound ligand:
Ligand SAH 3 x SAH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P41212
Unit cell:
a: 241.199Å b: 241.199Å c: 145.408Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.249 0.248 0.278
Expression system: Escherichia coli

Quick links

Citations

19 review citations

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

17 mentions without citation

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