› 1dk1

X-ray diffraction
2.8Å resolution

DETAILED VIEW OF A KEY ELEMENT OF THE RIBOSOME ASSEMBLY: CRYSTAL STRUCTURE OF THE S15-RRNA COMPLEX

Released:
DOI: 10.2210/pdb1dk1/pdb
PDB entry 1dk1 coloured by chain, front view.
PDB entry 1dk1 coloured by chain, side view.
PDB entry 1dk1 coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
Crystal structure of the S15-rRNA complex.
Nikulin A, Serganov A, Ennifar E, Tishchenko S, Nevskaya N, Shepard W, Portier C, Garber M, Ehresmann B, Ehresmann C, Nikonov S, Dumas P
Nat Struct Biol 7 273-7 (2000)
PMID: 10742169

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160398 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Small ribosomal subunit protein uS15 Chain: A
Molecule details ›
Chain: A
Length: 86 amino acids
Theoretical weight: 10.5 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P80378 (Residues: 2-87; Coverage: 97%)
Gene names: rps15, rpsO
Sequence domains: Ribosomal protein S15
Structure domains: S15/NS1, RNA-binding
RRNA FRAGMENT Chain: B
Molecule details ›
Chain: B
Length: 57 nucleotides
Theoretical weight: 18.46 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli

Ligands and Environments

3 bound ligands:
Ligand MG 9 x MG
Ligand NA 2 x NA
Ligand K 1 x K
1 modified residue:
Ligand MSE 4 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7A
Spacegroup: P6422
Unit cell:
a: 128.8Å b: 128.8Å c: 65.1Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.213 0.213 0.291
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Dynamics-based amplification of RNA function and its characterization by using NMR spectroscopy.
Al-Hashimi HM. (2005)
6 more

11 mentions without citation

Computational approaches to 3D modeling of RNA.
Laing et al. (2010)
10 more