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Crystal structure of box C/D RNP with 12 nt guide regions and 13 nt substrates

X-ray diffraction
3.604Å resolution
PDB entry 5gio coloured by chain, front view.
PDB entry 5gio coloured by chain, side view.
PDB entry 5gio coloured by chain, top view.
Source organism: Saccharolobus solfataricus
Assembly composition:
hetero decamer (preferred)
Entry contents: 3 distinct polypeptide molecules
2 distinct RNA molecules

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Assemblies

Assembly 1
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Multimeric state: hetero decamer
Accessible surface area: 64153.76 Å2
Buried surface area: 33565.48 Å2
Dissociation area: 3,298.11 Å2
Dissociation energy (ΔGdiss): 46.03 kcal/mol
Dissociation entropy (TΔSdiss): 25.22 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-157330
Assembly 2 (preferred)
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Multimeric state: hetero decamer
Accessible surface area: 63428.9 Å2
Buried surface area: 33593.63 Å2
Dissociation area: 3,314.05 Å2
Dissociation energy (ΔGdiss): 49.37 kcal/mol
Dissociation entropy (TΔSdiss): 25.22 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-157330

Macromolecules

Nop domain-containing protein
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: 1-1, 4-380; Coverage: 92%)
Gene name: SSO0939
Pfam:
InterPro:
CATH:
Nop domain-containing protein in PDB entry 5gio, assembly 2, front view.
Nop domain-containing protein in PDB entry 5gio, assembly 2, side view.
Nop domain-containing protein in PDB entry 5gio, assembly 2, top view.
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Large ribosomal subunit protein eL8
Chains: C, D, L
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
Pfam: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
InterPro:
CATH: 60s Ribosomal Protein L30; Chain: A;
Large ribosomal subunit protein eL8 in PDB entry 5gio, assembly 2, front view.
Large ribosomal subunit protein eL8 in PDB entry 5gio, assembly 2, side view.
Large ribosomal subunit protein eL8 in PDB entry 5gio, assembly 2, top view.
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Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
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: 1-1, 3-232; Coverage: 100%)
Gene names: C33_014, SSO0940, flpA
Pfam: Fibrillarin
InterPro:
CATH:
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase in PDB entry 5gio, assembly 2, front view.
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase in PDB entry 5gio, assembly 2, side view.
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase in PDB entry 5gio, assembly 2, top view.
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RNA chains G, H, N
Name: C/D RNA
Representative chains: G, H, N
Length: 40 nucleotides
Theoretical weight: 12.85 KDa
C/D RNA in PDB entry 5gio, assembly 2, front view.
C/D RNA in PDB entry 5gio, assembly 2, side view.
C/D RNA in PDB entry 5gio, assembly 2, top view.
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RNA chains I, J, O
Name: substrate
Representative chains: I, J, O
Length: 13 nucleotides
Theoretical weight: 4.18 KDa
substrate in PDB entry 5gio, assembly 2, front view.
substrate in PDB entry 5gio, assembly 2, side view.
substrate in PDB entry 5gio, assembly 2, top view.
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