› 3bnr

X-ray diffraction
2.1Å resolution

Crystal Structure of the Homo sapiens Mitochondrial Ribosomal Decoding Site in the presence of nonspecifically bound paromomycin (A1555G mutant, Br-derivative)

Released:
DOI: 10.2210/pdb3bnr/pdb
PDB entry 3bnr coloured by chain, front view.
PDB entry 3bnr coloured by chain, side view.
PDB entry 3bnr coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates.
Kondo J, Westhof E
Nucleic Acids Res 36 2654-66 (2008)
PMID: 18346970

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-219685 (preferred)
Entry contents:
3 distinct RNA molecules
Macromolecules (3 distinct):
A site of human mitochondrial ribosome, chain one Chains: A, C
Molecule details ›
Chains: A, C
Length: 23 nucleotides
Theoretical weight: 7.39 KDa
Source organism: Synthetic construct
Expression system: Not provided
A site of human mitochondrial ribosome, chain two Chain: B
Molecule details ›
Chain: B
Length: 22 nucleotides
Theoretical weight: 7.09 KDa
Source organism: Synthetic construct
Expression system: Not provided
A site of human mitochondrial ribosome, chain three Chain: D
Molecule details ›
Chain: D
Length: 21 nucleotides
Theoretical weight: 6.78 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand K 2 x K
Ligand PAR 1 x PAR
1 modified residue:
Ligand 5BU 4 x 5BU

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: C2
Unit cell:
a: 71.189Å b: 77.38Å c: 56.322Å
α: 90° β: 115.12° γ: 90°
R-values:
R R work R free
0.215 0.215 0.245
Expression system: Not provided

Quick links

Citations

6 review citations

The future of aminoglycosides: the end or renaissance?
Houghton et al. (2010)
5 more

1 mention without citation

The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates.
Kondo et al. (2008)