3I1Q: Crystal Structure Of The E. Coli 70s Ribosome In An Intermediate State Of Ratcheting

Citation:
Abstract
Protein biosynthesis on the ribosome requires repeated cycles of ratcheting, which couples rotation of the two ribosomal subunits with respect to each other, and swiveling of the head domain of the small subunit. However, the molecular basis for how the two ribosomal subunits rearrange contacts with each other during ratcheting while remaining stably associated is not known. Here, we describe x-ray crystal structures of the intact Escherichia coli ribosome, either in the apo-form (3.5 angstrom resolution) or with one (4.0 angstrom resolution) or two (4.0 angstrom resolution) anticodon stem-loop tRNA mimics bound, that reveal intermediate states of intersubunit rotation. In the structures, the interface between the small and large ribosomal subunits rearranges in discrete steps along the ratcheting pathway. Positioning of the head domain of the small subunit is controlled by interactions with the large subunit and with the tRNA bound in the peptidyl-tRNA site. The intermediates observed here provide insight into how tRNAs move into the hybrid state of binding that precedes the final steps of mRNA and tRNA translocation.
MMDB ID: 99487
PDB Deposition Date: 2009/6/27
Updated in MMDB: 2012/08
Experimental Method:
x-ray diffraction
Resolution: 3.81  Å
Source Organism:
Escherichia coli K-12
Similar Structures:
Merged PDB IDs:3I1Q 3I1R 3I1S 3I1T
Asymmetric Unit for 3I1Q: 108-meric
Molecular Components in 3I1Q
Label Count Molecule
Proteins (98 molecules)
2
30S Ribosomal Protein S2
Molecule annotation
2
30S Ribosomal Protein S3
Molecule annotation
2
30S Ribosomal Protein S4
Molecule annotation
2
30S Ribosomal Protein S5
Molecule annotation
2
30S Ribosomal Protein S6
Molecule annotation
2
30S Ribosomal Protein S7
Molecule annotation
2
30S Ribosomal Protein S8
Molecule annotation
2
30S Ribosomal Protein S9
Molecule annotation
2
30S Ribosomal Protein S10
Molecule annotation
2
30S Ribosomal Protein S11
Molecule annotation
2
30S Ribosomal Protein S12
Molecule annotation
2
30S Ribosomal Protein S13
Molecule annotation
2
30S Ribosomal Protein S14
Molecule annotation
2
30S Ribosomal Protein S15
Molecule annotation
2
30S Ribosomal Protein S16
Molecule annotation
2
30S Ribosomal Protein S17
Molecule annotation
2
30S Ribosomal Protein S18
Molecule annotation
2
30S Ribosomal Protein S19
Molecule annotation
2
30S Ribosomal Protein S20
Molecule annotation
2
30S Ribosomal Protein S21
Molecule annotation
2
50S Ribosomal Protein L2
Molecule annotation
2
50S Ribosomal Protein L3
Molecule annotation
2
50S Ribosomal Protein L4
Molecule annotation
2
50S Ribosomal Protein L5
Molecule annotation
2
50S Ribosomal Protein L6
Molecule annotation
2
50S Ribosomal Protein L9
Molecule annotation
2
50S Ribosomal Protein L11
Molecule annotation
2
50S Ribosomal Protein L13
Molecule annotation
2
50S Ribosomal Protein L14
Molecule annotation
2
50S Ribosomal Protein L15
Molecule annotation
2
50S Ribosomal Protein L16
Molecule annotation
2
50S Ribosomal Protein L17
Molecule annotation
2
50S Ribosomal Protein L18
Molecule annotation
2
50S Ribosomal Protein L19
Molecule annotation
2
50S Ribosomal Protein L20
Molecule annotation
2
50S Ribosomal Protein L21
Molecule annotation
2
50S Ribosomal Protein L22
Molecule annotation
2
50S Ribosomal Protein L23
Molecule annotation
2
50S Ribosomal Protein L24
Molecule annotation
2
50S Ribosomal Protein L25
Molecule annotation
2
50S Ribosomal Protein L27
Molecule annotation
2
50S Ribosomal Protein L28
Molecule annotation
2
50S Ribosomal Protein L29
Molecule annotation
2
50S Ribosomal Protein L30
Molecule annotation
2
50S Ribosomal Protein L32
Molecule annotation
2
50S Ribosomal Protein L33
Molecule annotation
2
50S Ribosomal Protein L34
Molecule annotation
2
50S Ribosomal Protein L35
Molecule annotation
2
50S Ribosomal Protein L36
Molecule annotation
Nucleotides(5 molecules)
2
16S rRNA
Molecule annotation
2
P-site tRNA ASL Fragment
Molecule annotation
2
Messenger RNA
Molecule annotation
2
23S rRNA
Molecule annotation
2
5S rRNA
Molecule annotation
Chemicals (365 molecules)
1
363
2
2
* Click molecule labels to explore molecular sequence information.

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