› 3nvk

X-ray diffraction
3.21Å resolution

Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle

Released:
DOI: 10.2210/pdb3nvk/pdb
PDB entry 3nvk coloured by chain, front view.
PDB entry 3nvk coloured by chain, side view.
PDB entry 3nvk 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

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-186391 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (5 distinct):
Nop domain-containing protein Chains: A, F
Molecule details ›
Chains: A, F
Length: 376 amino acids
Theoretical weight: 43.47 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U4M1 (Residues: 1-363; Coverage: 90%)
Gene name: PF0060
Sequence domains:
Structure domains:
Large ribosomal subunit protein eL8 Chains: E, H
Molecule details ›
Chains: E, H
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;
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase Chains: I, J
Molecule details ›
Chains: I, J
Length: 234 amino acids
Theoretical weight: 26.76 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8U4M2 (Residues: 1-227; Coverage: 100%)
Gene names: PF0059, flpA
Sequence domains: Fibrillarin
Structure domains:
RNA (5'-R(*GP*CP*CP*GP*UP*UP*GP*AP*AP*GP*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: K, L
Molecule details ›
Chains: K, L
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: G, S
Molecule details ›
Chains: G, S
Length: 13 nucleotides
Theoretical weight: 4.16 KDa

Ligands and Environments

1 bound ligand:
Ligand SAM 2 x SAM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID, APS BEAMLINE 23-BM-B
Spacegroup: P21212
Unit cell:
a: 330.039Å b: 94.548Å c: 97.729Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.23 0.288
Expression system: Escherichia coli

Quick links

Citations

7 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)
6 more

1 mention without citation

Structural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle.
Xue et al. (2010)