› 3nvi

X-ray diffraction
2.71Å resolution

Structure of N-terminal truncated Nop56/58 bound with L7Ae and box C/D RNA

Released:
DOI: 10.2210/pdb3nvi/pdb
PDB entry 3nvi coloured by chain, front view.
PDB entry 3nvi coloured by chain, side view.
PDB entry 3nvi coloured by chain, top view.
Source organism: Pyrococcus furiosus DSM 3638
Primary publication:
Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle.
Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H
Mol Cell 39 939-49 (2010)
PMID: 20864039

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero hexamer
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186387 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
Nop domain-containing protein Chains: A, C
Molecule details ›
Chains: A, C
Length: 379 amino acids
Theoretical weight: 43.94 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U4M1 (Residues: 1-369; Coverage: 92%)
Gene name: PF0060
Sequence domains:
Structure domains:
Large ribosomal subunit protein eL8 Chains: B, D
Molecule details ›
Chains: B, D
Length: 129 amino acids
Theoretical weight: 14.24 KDa
Source organism: Pyrococcus furiosus DSM 3638
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;
RNA (5'-R(*CP*UP*CP*UP*GP*AP*CP*CP*GP*AP*AP*AP*GP*GP*CP*GP*UP*GP*AP*UP*GP*AP*GP*C)-3') Chains: E, F
Molecule details ›
Chains: E, F
Length: 24 nucleotides
Theoretical weight: 7.75 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID, APS BEAMLINE 22-BM
Spacegroup: P212121
Unit cell:
a: 87.216Å b: 91.841Å c: 155.603Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.249
Expression system: Escherichia coli

Quick links

Citations

6 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)
5 more

8 mentions without citation

Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P.
Samanta et al. (2016)
7 more