A ratchet-like inter-subunit reorganization of the ribosome during translocation

  title={A ratchet-like inter-subunit reorganization of the ribosome during translocation},
  author={Joachim Frank and Rajendra K. Agrawal},
The ribosome is a macromolecular assembly that is responsible for protein biosynthesis following genetic instructions in all organisms. It is composed of two unequal subunits: the smaller subunit binds messenger RNA and the anticodon end of transfer RNAs, and helps to decode the mRNA; and the larger subunit interacts with the amino-acid-carrying end of tRNAs and catalyses the formation of the peptide bonds. After peptide-bond formation, elongation factor G (EF-G) binds to the ribosome… 

Molecular mechanics of 30S subunit head rotation

Comparative structure analysis across 55 ribosome structures shows that 30S head movement results from flexing at two hinge points lying within conserved elements of 16S rRNA, which explains the mode of action of spectinomycin, an antibiotic that blocks translocation by binding to hinge 2.

Structure of the ribosome with elongation factor G trapped in the pretranslocation state

A model in which domain IV of EF-G promotes the translocation of tRNA from the A to the P site as the small ribosome subunit spontaneously rotates back from the hybrid, rotated state into the nonrotated posttranslocation state is suggested.

Head swivel on the ribosome facilitates translocation via intra-subunit tRNA hybrid sites

Cryoelectron microscopy analysis is used to resolve two previously unseen subpopulations within Thermus thermophilus EF-G–ribosome complexes at subnanometre resolution and provides direct structural and mechanistic insight into the ‘missing link’ in terms of tRNA intermediates involved in the universally conserved translocation process.

Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: Functional implications

A three-dimensional cryo-electron microscopic map of a complex of the Escherichia coli 70S ribosome and RRF is obtained, finding that RRF interacts mainly with the segments of the large ribosomal subunit's (50S) rRNA helices that are involved in the formation of two central intersubunit bridges, B2a and B3.

Ribosomal crystallography: peptide bond formation and its inhibition.

The rotatory motion is the major component of unified machinery for peptide-bond formation, translocation, and nascent protein progression, since its spiral nature ensures the entrance of the nascent peptide into the ribosomal exit tunnel.

Elongation Factor G Bound to the Ribosome in an Intermediate State of Translocation

Comparison with the posttranslocational state suggests that interactions between the tRNA and L1 stalk are preserved throughout translocation and that these are probably an essential feature of translocation required for stabilization of the hybrid P/E state.

The Ribosome as an RNA-Based Molecular Machine

The binding of functional ligands, such as aminoacyl-tRNA and an elongation factor with GTP, and the chemical reactions of transpeptidation and GTP hydrolysis play the role of a Maxwell's Demon: they rectify the random fluctuations to produce the unidirectional conveyance process and translation.

Following movement of domain IV of elongation factor G during ribosomal translocation

This work follows the movement of domain IV of EF-G, which is critical for the catalysis of translocation, relative to protein S12 of the small ribosomal subunit using single-molecule FRET and shows that ribosome-boundEF-G adopts distinct conformations corresponding to the pre- and posttranslocation states of the ribosomes.



Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation.

Three-dimensional cryo-electron microscopy has visualized elongation factor G in a ribosome-EF-G-GDP-fusidic acid complex, revealing a large conformational change mainly associated with domain IV, the domain that mimics the shape of the anticodon arm of the tRNA in the structurally homologous ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog.

Visualization of elongation factor Tu on the Escherichia coli ribosome

Electron cryomicroscopy and angular reconstitution are used to visualize directly the kirromycin-stalled ternary complex in the A site of the 70S ribosome of Escherichia coli and three-dimensional reconstruction at 18 Å resolution shows the ternaries spanning the inter-subunit space with the acceptor domain of the tRNA reaching into the decoding centre.

Translocation in Protein Synthesis: A Hybrid Structure Model

The whole process of peptide synthesis is catalysed by at least three enzymes and requires guanosine triphosphate (GTP)15,16.

Molecular Movement inside the Translational Engine

Studies of Elongation Factor G-Dependent tRNA Translocation by Three-Dimensional Cryo-Electron Microscopy

The results conclusively show that a number of ribosomal regions undergo a change of conformation upon EF-G binding, and it appears that they use the same anchoring points on the ribosome and make contact with the same GTPase-associated center while differing substantially in their functions.

Crystal Structure of the Ternary Complex of Phe-tRNAPhe, EF-Tu, and a GTP Analog

The overall shape of the ternary complex is similar to that of the translocation factor, EF-G-GDP, and this suggests a novel mechanism involving “molecular mimicry” in the translational apparatus.

Solution Structure of the E. coli 70S Ribosome at 11.5 Å Resolution

X-ray crystal structures of 70S ribosome functional complexes.

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

Conformational variability in Escherichia coli 70S ribosome as revealed by 3D cryo-electron microscopy.