› 1mji

X-ray diffraction
2.5Å resolution

DETAILED ANALYSIS OF RNA-PROTEIN INTERACTIONS WITHIN THE BACTERIAL RIBOSOMAL PROTEIN L5/5S RRNA COMPLEX

Released:
DOI: 10.2210/pdb1mji/pdb
PDB entry 1mji coloured by chain, front view.
PDB entry 1mji coloured by chain, side view.
PDB entry 1mji coloured by chain, top view.
Source organisms:
Primary publication:
Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.
Perederina A, Nevskaya N, Nikonov O, Nikulin A, Dumas P, Yao M, Tanaka I, Garber M, Gongadze G, Nikonov S
RNA 8 1548-57 (2002)
PMID: 12515387

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154300 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Large ribosomal subunit protein uL5 Chains: A, B
Molecule details ›
Chains: A, B
Length: 182 amino acids
Theoretical weight: 21.16 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P41201 (Residues: 1-182; Coverage: 100%)
Gene names: rpl5, rplE
Sequence domains:
Structure domains: 50s Ribosomal Protein L5; Chain: A,
5S rRNA fragment Chains: C, D
Molecule details ›
Chains: C, D
Length: 34 nucleotides
Theoretical weight: 10.85 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P21
Unit cell:
a: 51.89Å b: 99.6Å c: 65.73Å
α: 90° β: 100.05° γ: 90°
R-values:
R R work R free
0.21 0.21 0.288
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Specific features of 5S rRNA structure - its interactions with macromolecules and possible functions.
Smirnov et al. (2008)
3 more

13 mentions without citation

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