› 1y69

X-ray diffraction
3.33Å resolution

RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans

Released:
DOI: 10.2210/pdb1y69/pdb
PDB entry 1y69 coloured by chain, front view.
PDB entry 1y69 coloured by chain, side view.
PDB entry 1y69 coloured by chain, top view.
Source organisms:
Primary publication:
X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.
Wilson DN, Schluenzen F, Harms JM, Yoshida T, Ohkubo T, Albrecht R, Buerger J, Kobayashi Y, Fucini P
EMBO J 24 251-60 (2005)
PMID: 15616575

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-141649 (preferred)
Entry contents:
3 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (5 distinct):
Large ribosomal subunit protein uL16 Chain: K
Molecule details ›
Chain: K
Length: 141 amino acids
Theoretical weight: 16.13 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RXJ5 (Residues: 1-141; Coverage: 100%)
Gene names: DR_0318, rplP
Sequence domains: Ribosomal protein L16p/L10e
Structure domains: Ribosomal protein L10e/L16
Large ribosomal subunit protein bL27 Chain: U
Molecule details ›
Chain: U
Length: 91 amino acids
Theoretical weight: 9.61 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
UniProt:
  • Canonical: Q9RY65 (Residues: 1-91; Coverage: 100%)
Gene names: DR_0085, rpmA
Sequence domains: Ribosomal L27 protein
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Ribosome-recycling factor Chain: 8
Molecule details ›
Chain: 8
Length: 113 amino acids
Theoretical weight: 12.84 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A805 (Residues: 1-30, 106-185; Coverage: 60%)
Gene names: JW0167, b0172, frr, rrf
Sequence domains: Ribosome recycling factor
Structure domains: Ribosome-recycling factor
23S ribosomal RNA Chain: 0
Molecule details ›
Chain: 0
Length: 2880 nucleotides
Theoretical weight: 933.41 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: 9
Molecule details ›
Chain: 9
Length: 124 nucleotides
Theoretical weight: 39.91 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: I222
Unit cell:
a: 168.7Å b: 405Å c: 693Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.291 0.275 0.338
Expression system: Escherichia coli

Quick links

Citations

12 review citations

What recent ribosome structures have revealed about the mechanism of translation.
Schmeing et al. (2009)
11 more

2 mentions without citation

X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.
Wilson et al. (2005)
1 more