## 3 Structural Snapshots of tRNA Conformation Plasticity during Translation  
### Initiation  
Briefly, during translation initiation in prokaryotes, the 30S small subunit binds to the initiator tRNA (fMet-tRNAMet), initiation factors (IF1, IF2 and IF3) and mRNA to form the 30S pre-initiation complex in a multi-step process. Once the mRNA is correctly positioned, and the anticodon of the initiator tRNA is base-paired with the initiation AUG codon of the mRNA, sequential release of the factors (mediated by IF2's GTP hydrolysis) promotes the association of the 50S large subunit to form the initiation 70S complex [69, 70, 71, 72, 73, 74, 75]. CryoEM analysis of initiation 70S complexes has shown that the initiator tRNA is held in a characteristic position by two interactions: One involving the anticodon stem which is hidden in the P site of the small subunit, and the other between IF2 and the tRNA acceptor stem [76, 77]. The orientation of initiator tRNA differs from the canonical P site position as the \(C\)-terminal domain of IF2 sterically precludes a \"classical\" P site binding of the initiator tRNA molecule, and instead, forces the tRNA to acquire an intermediate configuration (termed P/I) between the classical P and hybrid P/E sites [76]. The structures also suggested a \(\sim\)20\({}^{\circ}\) rotation of the ASL, which displaces that CCA end by 28 A towards the E site. On the contrary, more recent cryoEM analysis of 30S initiation complexes showed that the CCA end of the tRNA was instead oriented towards the A site [78]. This new state, called P/I1, showed a rotation of \(\sim\)15\({}^{\circ}\) of the acceptor stem. A somewhat different P/I state was also reported for the 30S IC from _T. thermophilus_ in the absence of IF3 [79], which may be related to IF3's role in the stability of tRNA binding to the initiation complex. The eukaryotic initiation of translation, a highly regulated stage, is a very complex process as it involves 11-13 eIFs. Whereas procaryotes can use the SD (Shine-Dalgarno) sequence present in more than 40% of all bacterial genes to locate the start codon [73, 80, 81, 82], eukaryotic ribosomes use a scanning mechanism [83]. During the initial stage of initiation, the 40S small subunit, supervised by initiation factors eIF1, eIF1A and eIF3 binds to the ternary complex (TC) formed by eIF2, GTP and initiator tRNA. The subsequent cap-dependent interaction of this 43S complex with the 5' end of the mRNA is guided by another factor, eIF4E, as well as eIF4 Ga and polyA binding protein (PABP), that interact with the 3' end. The next step, in which initiation factors eIF4A, eIF2 and eIF5 play a role, involves the formation of the 48S complex (at this point, the initiator tRNA is already base-paired to the start codon). The next stages in the formation of the 80S initiation ribosome complex entangle the binding to the 60S large subunit, hydrolysis of GTP by eIF5B and subsequent release of the factors to correctly place the initiator tRNA in its final position [83, 84, 85, 86, 87, 88]. Initial low resolution studies (e.g., [89, 90]) have led the way to higher resolution studies that have provided relevant snapshots of the eukaryotic initiation process. These structures include complexes formed by 40S-elF1 [91], 40S-elF1-elF1A [92] and 60S-elF6 [93] from _Tetrahymena thermophila_, mamalian 40S-elF1-elF1A [94] and 43S complex formed by eIF3, TC and Dhx29 (an RNA helicase), but without mRNA, eIF1, eIF1A or eIF5 [95], as well as yeast _S. cerevisiae_ 40S-elF1-elF3 [96] and _Kluyveromyces lactis_ 48S complexes containing eIF1, eIF1A, mRNA, and the TC complex formed by eIF2, GTP and initiator tRNA [97]. These structures show that the 40S binding site for eIF1 sterically impedes the standard P site binding of the initiator tRNA molecule, as it happens in prokaryotes.