PDBe 3nmu

X-ray diffraction
2.73Å resolution

Crystal Structure of substrate-bound halfmer box C/D RNP

Released:

Function and Biology Details

Structure analysis Details

Assemblies composition:
hetero pentamer (preferred)
hetero decamer
Entry contents:
3 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (5 distinct):
Nop domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 379 amino acids
Theoretical weight: 43.94 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U4M1 (Residues: 1-369; Coverage: 92%)
Gene name: PF0060
Sequence domains: snoRNA binding domain, fibrillarin
Structure domains:
50S ribosomal protein L7Ae Chains: C, G
Molecule details ›
Chains: C, G
Length: 129 amino acids
Theoretical weight: 14.24 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U160 (Residues: 2-123; Coverage: 99%)
Gene names: PF1367, 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: F, J
Molecule details ›
Chains: F, J
Length: 234 amino acids
Theoretical weight: 26.76 KDa
Source organism: Pyrococcus furiosus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U4M2 (Residues: 1-227; Coverage: 100%)
Gene names: PF0059, flpA
Sequence domains: Fibrillarin
Structure domains:
RNA (34-MER) Chains: D, E
Molecule details ›
Chains: D, E
Length: 34 nucleotides
Theoretical weight: 11.01 KDa
RNA (5'-R(*GP*AP*GP*CP*UP*UP*CP*AP*AP*CP*GP*GP*C)-3') Chains: I, K
Molecule details ›
Chains: I, K
Length: 13 nucleotides
Theoretical weight: 4.16 KDa

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 293.506Å b: 94.054Å c: 96.81Å
α: 90° β: 101.47° γ: 90°
R-values:
R R work R free
0.224 0.222 0.284
Expression system: Escherichia coli