The complexity of rotational motions in the ribosome has inspired a number of efforts to quantitatively distinguish between rotation states. See Movie S1 for a summary of head rotations. For additional visual comparisons of SSU body and SSU head rotation and tilting, see Supplementary Figures S1 and S2. ( C) Head tilting shown for ψ head = 90°, which corresponds to the head moving in the direction of the A site. ( B) Head tilting shown for tilt direction ψ head = 0°, which corresponds roughly to tilting about the mRNA binding track along the A, P and E sites (see Supplementary Figure S10). In eukaryotic ribosomes, tilt-like rotations have been described as ‘rolling’. ( B) During the elongation cycle, the SSU rotates about an axis |$\vec$| (i.e. rRNA of the bacterial ribosome is shown in a classical unrotated conformation (RCSB ID: 4V9D ( 32) chains DA, BA). ( A) All ribosomes are composed of two subunits, called the large subunit (LSU white) and the small subunit (SSU cyan). Together, this rapidly growing body of data is demonstrating the various ways that rotary-like rearrangements in the ribosome are integral to protein synthesis. To complement structural studies, numerous single-molecule ( 16–20) and bulk measurements ( 21–26) have provided insights into the relationship between subunit rotation and tRNA rearrangements during translation. The range of accessible domain motions is further highlighted by simulations of tRNA–mRNA translocation ( 14) and structures of tmRNA complex ( 15), where tilt-like rotations of the SSU head are also apparent. Other studies have found that the ‘head’ domain of the SSU (Figure 1C, D) rotates relative to the SSU ‘body’ in prokaryotic and eukaryotic ribosomes, a motion referred to as ‘swiveling’ ( 9–13). More than a decade later, studies of eukaryotic ribosomes ( 8) showed that the SSU may also undergo tilt-like rotation (i.e. ‘rolling’ Figure 2). In early studies, cryogenic electron microscopy (cryo-EM) reconstructions visualized a ratchet-like rotation of the small subunit (SSU Figure 1B), relative to the large subunit (LSU) ( 7). Over the last 20 years, revolutionary advances in structure determination have allowed for a range of ribosomal subunit orientations to be identified. While such conformational rearrangements are necessary to sustain cellular life, their large scale and complex character pose a significant challenge to identifying the mechanistic properties that govern translation. These steps are also often accompanied by global reorganization events in the ribosome. At a larger scale, the flexibility of tRNA molecules allows them to navigate an intricate series of rearrangements (10–100 Å, each) ( 4–6) as they are delivered to the ribosome, transition between ribosomal tRNA-binding sites and then dissociate. At various stages of function, there are essential small-scale rearrangements, such as movement of a switch loop during translational EF-Tu activation ( 1), displacement of the 3’-CCA tail of tRNA during peptide bond formation ( 2) or ribosomal RNA (rRNA) base-flipping and 30S head domain closure during mRNA decoding ( 3). Many conformational changes in the ribosome are required during protein synthesis. Together, this study establishes a common foundation with which structural, simulation, single-molecule and biochemical efforts can more precisely interrogate the dynamics of this prototypical molecular machine. As another example, domain orientations associated with frameshifting in bacteria are similar to those found in eukaryotic ribosomes. ‘rolling’) are pervasive in both prokaryotic and eukaryotic (cytosolic and mitochondrial) ribosomes. For example, we show that tilt-like rearrangements of the SSU body (i.e. This reveals aspects of subunit rearrangements that are universal, and others that are organism/domain-specific. By considering the entire RCSB PDB database, we describe 1208 fully-assembled ribosome complexes and 334 isolated small subunits, which span >50 species. To overcome this, we developed an approach where the orientation of each SSU head and body is described in terms of three angular coordinates (rotation, tilt and tilt direction) and a single translation. However, with nearly 2000 structures of ribosomes and ribosomal subunits now publicly available, it is exceedingly difficult to design experiments based on analysis of all known rotation states. 2) Create representations of the selected molecule.Protein synthesis by the ribosome requires large-scale rearrangements of the ‘small’ subunit (SSU ∼1 MDa), including inter- and intra-subunit rotational motions. The Graphical Representations tab allows you to modify the visual representation of your model.
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