› 486d

X-ray diffraction
7.5Å resolution

X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES

Released:
DOI: 10.2210/pdb486d/pdb
PDB entry 486d coloured by chain, front view.
PDB entry 486d coloured by chain, side view.
PDB entry 486d coloured by chain, top view.
Source organisms:
Primary publication:
X-ray crystal structures of 70S ribosome functional complexes.
Cate JH, Yusupov MM, Yusupova GZ, Earnest TN, Noller HF
Science 285 2095-104 (1999)
PMID: 10497122

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195824 (preferred)
Entry contents:
7 distinct RNA molecules
Macromolecules (7 distinct):
P-SITE TRNA OF 70S RIBOSOME Chain: A
Molecule details ›
Chain: A
Length: 74 nucleotides
Theoretical weight: 24.16 KDa
Source organism: Escherichia coli
Sequence domains: tRNA
P-SITE CODON OF 70S RIBOSOME Chain: B
Molecule details ›
Chain: B
Length: 3 nucleotides
Theoretical weight: 874 Da
Source organism: Synthetic construct
Expression system: Not provided
A-SITE TRNA OF 70S RIBOSOME Chain: C
Molecule details ›
Chain: C
Length: 72 nucleotides
Theoretical weight: 23.33 KDa
Source organism: Saccharomyces cerevisiae
Sequence domains: tRNA
A-SITE CODON OF 70S RIBOSOME Chain: D
Molecule details ›
Chain: D
Length: 3 nucleotides
Theoretical weight: 912 Da
Source organism: Synthetic construct
Expression system: Not provided
E-SITE TRNA OF 70S RIBOSOME Chain: E
Molecule details ›
Chain: E
Length: 72 nucleotides
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus
Sequence domains: tRNA
PENULTIMATE STEM OF 16S RRNA IN THE 70S RIBOSOME Chain: F
Molecule details ›
Chain: F
Length: 85 nucleotides
Theoretical weight: 27.51 KDa
Source organism: Thermus thermophilus
900 STEM-LOOP OF 16S RRNA IN THE 70S RIBOSOME Chain: G
Molecule details ›
Chain: G
Length: 33 nucleotides
Theoretical weight: 10.71 KDa
Source organism: Thermus thermophilus

Ligands and Environments

1 bound ligand:
Ligand IR 4 x IR
11 modified residues:
Ligand PSU 7 x PSU
Ligand H2U 6 x H2U
Ligand M2G 2 x M2G
Ligand OMC 1 x OMC
Ligand YYG 1 x YYG
Ligand 5MC 4 x 5MC
Ligand 5MU 3 x 5MU
Ligand 2MG 1 x 2MG
Ligand 1MG 2 x 1MG
Ligand 7MG 1 x 7MG
Ligand 1MA 1 x 1MA

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: I422
Unit cell:
a: 508.02Å b: 508.02Å c: 802.79Å
α: 90° β: 90° γ: 90°
Expression system: Not provided

Quick links

Citations

98 review citations

Structural insights into translational fidelity.
Ogle et al. (2005)
97 more

6 mentions without citation

Aminoglycosides: perspectives on mechanisms of action and resistance and strategies to counter resistance.
Kotra et al. (2000)
5 more