486D image
Deposition Date 1999-09-09
Release Date 1999-10-04
Last Version Date 2023-09-13
Entry Detail
PDB ID:
486D
Keywords:
RIBOSOME
Title:
X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES
Biological Source:
Source Organism:
(Taxon ID: )Escherichia coli (Taxon ID: 562)
Saccharomyces cerevisiae (Taxon ID: 4932)
Thermus thermophilus (Taxon ID: 274)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
7.50 Å
Space Group:
I 4 2 2
486D validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:P-SITE TRNA OF 70S RIBOSOME
Chain IDs:A
Chain Length:74
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:P-SITE CODON OF 70S RIBOSOME
Chain IDs:B
Chain Length:3
Number of Molecules:1
Biological Source:
Polymer Type:polyribonucleotide
Molecule:A-SITE TRNA OF 70S RIBOSOME
Chain IDs:C
Chain Length:72
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:A-SITE CODON OF 70S RIBOSOME
Chain IDs:D
Chain Length:3
Number of Molecules:1
Biological Source:
Polymer Type:polyribonucleotide
Molecule:E-SITE TRNA OF 70S RIBOSOME
Chain IDs:E
Chain Length:72
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:PENULTIMATE STEM OF 16S RRNA IN THE 70S RIBOSOME
Chain IDs:F
Chain Length:85
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:900 STEM-LOOP OF 16S RRNA IN THE 70S RIBOSOME
Chain IDs:G
Chain Length:33
Number of Molecules:1
Biological Source:Thermus thermophilus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MA C A ?
1MG C G 1N-METHYLGUANOSINE-5'-MONOPHOSPHATE
2MG C G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
5MC A C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE
5MU A U 5-METHYLURIDINE 5'-MONOPHOSPHATE
7MG C G ?
H2U A U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
M2G A G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
OMC A C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
PSU A U PSEUDOURIDINE-5'-MONOPHOSPHATE
YYG A G ?
Ligand Molecules
IR
Primary Citation
X-ray crystal structures of 70S ribosome functional complexes.
Science 285 2095 2104 (1999)
PMID: 10497122 DOI: 10.1126/science.285.5436.2095

Abstact

Structures of 70S ribosome complexes containing messenger RNA and transfer RNA (tRNA), or tRNA analogs, have been solved by x-ray crystallography at up to 7.8 angstrom resolution. Many details of the interactions between tRNA and the ribosome, and of the packing arrangements of ribosomal RNA (rRNA) helices in and between the ribosomal subunits, can be seen. Numerous contacts are made between the 30S subunit and the P-tRNA anticodon stem-loop; in contrast, the anticodon region of A-tRNA is much more exposed. A complex network of molecular interactions suggestive of a functional relay is centered around the long penultimate stem of 16S rRNA at the subunit interface, including interactions involving the "switch" helix and decoding site of 16S rRNA, and RNA bridges from the 50S subunit.

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Primary Citation of related structures
486D