5gip

X-ray diffraction
3.13Å resolution

Crystal structure of box C/D RNP with 13 nt guide regions and 11 nt substrates

Released:
Source organism: Saccharolobus solfataricus
Primary publication:
Box C/D guide RNAs recognize a maximum of 10 nt of substrates.
Proc Natl Acad Sci U S A 113 10878-83 (2016)
PMID: 27625427

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-157331 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (5 distinct):
Nop domain-containing protein Chains: A, B, K, L
Molecule details ›
Chains: A, B, K, L
Length: 388 amino acids
Theoretical weight: 44.17 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97ZH3 (Residues: 1-1, 4-380; Coverage: 92%)
Gene name: SSO0939
Sequence domains:
Structure domains:
Large ribosomal subunit protein eL8 Chains: C, D, M, N
Molecule details ›
Chains: C, D, M, N
Length: 130 amino acids
Theoretical weight: 14.08 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: P55858 (Residues: 3-127; Coverage: 98%)
Gene names: C04_031, SSO0091, 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, O, P
Molecule details ›
Chains: E, F, O, P
Length: 232 amino acids
Theoretical weight: 26.44 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: P58032 (Residues: 1-1, 3-232; Coverage: 100%)
Gene names: C33_014, SSO0940, flpA
Sequence domains: Fibrillarin
Structure domains:
C/D RNA Chains: G, H, Q, R
Molecule details ›
Chains: G, H, Q, R
Length: 41 nucleotides
Theoretical weight: 13.2 KDa
substrate Chains: I, J, S, T
Molecule details ›
Chains: I, J, S, T
Length: 11 nucleotides
Theoretical weight: 3.48 KDa

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P1
Unit cell:
a: 97.916Å b: 97.718Å c: 128.793Å
α: 108.98° β: 104.42° γ: 89.86°
R-values:
R R work R free
0.18 0.178 0.234
Expression system: Escherichia coli