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Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome.

Fernández IS, Bai XC, Murshudov G, Scheres SH, Ramakrishnan V - Cell (2014)

Bottom Line: By using recent advances in single-particle electron cryomicroscopy, we have solved the structure of CrPV-IRES bound to the ribosome of the yeast Kluyveromyces lactis in both the canonical and rotated states at overall resolutions of 3.7 and 3.8 Å, respectively.In both states, the pseudoknot PKI of the CrPV-IRES mimics a tRNA/mRNA interaction in the decoding center of the A site of the 40S ribosomal subunit.Translocation of the IRES by elongation factor 2 (eEF2) is required to bring the first codon of the mRNA into the A site and to allow the start of translation.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.

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Resolutions for Overall Data Set and Individual Classes, Related to Figure 1Left: Gold standard Fourier shell correlation coefficients for the reconstructions of the classes shown in Figure S1. The dashed line represents an FSC of 0.143, and the resolution at which the FSC reaches this value is shown in each case. On the right, the local resolution is shown by color, with the surface shown to the left of the color bar, and a cross-section through the ribosome on the right. Throughout much of the interior, the local resolution is significantly better than the overall resolution.
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figs2: Resolutions for Overall Data Set and Individual Classes, Related to Figure 1Left: Gold standard Fourier shell correlation coefficients for the reconstructions of the classes shown in Figure S1. The dashed line represents an FSC of 0.143, and the resolution at which the FSC reaches this value is shown in each case. On the right, the local resolution is shown by color, with the surface shown to the left of the color bar, and a cross-section through the ribosome on the right. Throughout much of the interior, the local resolution is significantly better than the overall resolution.

Mentions: An initial reconstruction yielded an overall resolution of 3.5 Å (Figures S1 (top) and S2 available online). However, the map showed that there was considerable variability in the conformation of the small ribosomal subunit (40S), the CrPV-IRES (located at the intersubunit space), and the L1-stalk of the large ribosomal subunit. Maximum-likelihood particle sorting (Scheres, 2012b) was applied recursively to the data set, and several homogeneous subpopulations were clearly identified. Two major subpopulations corresponded to a rotated state of the ribosomal subunits (20%) and a ribosome in a canonical state (12.6%), with resolutions of 3.7 and 3.8 Å, respectively (Figures S1 (middle) and S2). These two states are similar to the canonical and rotated states of the ribosome observed during translocation (e.g., Agirrezabala et al., 2008; Julián et al., 2008; Tourigny et al., 2013). In both states, the CrPV-IRES folds into a well-defined 3D structure in the intersubunit space of the ribosome, in agreement with previous studies (Schüler et al., 2006).


Initiation of translation by cricket paralysis virus IRES requires its translocation in the ribosome.

Fernández IS, Bai XC, Murshudov G, Scheres SH, Ramakrishnan V - Cell (2014)

Resolutions for Overall Data Set and Individual Classes, Related to Figure 1Left: Gold standard Fourier shell correlation coefficients for the reconstructions of the classes shown in Figure S1. The dashed line represents an FSC of 0.143, and the resolution at which the FSC reaches this value is shown in each case. On the right, the local resolution is shown by color, with the surface shown to the left of the color bar, and a cross-section through the ribosome on the right. Throughout much of the interior, the local resolution is significantly better than the overall resolution.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4017093&req=5

figs2: Resolutions for Overall Data Set and Individual Classes, Related to Figure 1Left: Gold standard Fourier shell correlation coefficients for the reconstructions of the classes shown in Figure S1. The dashed line represents an FSC of 0.143, and the resolution at which the FSC reaches this value is shown in each case. On the right, the local resolution is shown by color, with the surface shown to the left of the color bar, and a cross-section through the ribosome on the right. Throughout much of the interior, the local resolution is significantly better than the overall resolution.
Mentions: An initial reconstruction yielded an overall resolution of 3.5 Å (Figures S1 (top) and S2 available online). However, the map showed that there was considerable variability in the conformation of the small ribosomal subunit (40S), the CrPV-IRES (located at the intersubunit space), and the L1-stalk of the large ribosomal subunit. Maximum-likelihood particle sorting (Scheres, 2012b) was applied recursively to the data set, and several homogeneous subpopulations were clearly identified. Two major subpopulations corresponded to a rotated state of the ribosomal subunits (20%) and a ribosome in a canonical state (12.6%), with resolutions of 3.7 and 3.8 Å, respectively (Figures S1 (middle) and S2). These two states are similar to the canonical and rotated states of the ribosome observed during translocation (e.g., Agirrezabala et al., 2008; Julián et al., 2008; Tourigny et al., 2013). In both states, the CrPV-IRES folds into a well-defined 3D structure in the intersubunit space of the ribosome, in agreement with previous studies (Schüler et al., 2006).

Bottom Line: By using recent advances in single-particle electron cryomicroscopy, we have solved the structure of CrPV-IRES bound to the ribosome of the yeast Kluyveromyces lactis in both the canonical and rotated states at overall resolutions of 3.7 and 3.8 Å, respectively.In both states, the pseudoknot PKI of the CrPV-IRES mimics a tRNA/mRNA interaction in the decoding center of the A site of the 40S ribosomal subunit.Translocation of the IRES by elongation factor 2 (eEF2) is required to bring the first codon of the mRNA into the A site and to allow the start of translation.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.

Show MeSH
Related in: MedlinePlus