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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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Interaction of the CrPV-IRES with the Decoding Center of the 40S Subunit(A) Overview of the CrPV-IRES-ribosome.(B) Superposition of the CrPV-IRES with A, P, and E site tRNAs (from 2J00, Selmer et al., 2006), showing that the green pseudoknot PKI of the IRES is in the decoding center normally occupied by an A site tRNA anticodon stem loop.(C) Details of the interaction of PKI of the IRES showing that the three highly conserved 18S rRNA bases G577, A1755, and A1756 (corresponding to G530, A1492, and A1493 in E. coli) change conformation from relative to the structure of the empty yeast ribosome (purple; Ben-Shem et al., 2011). In doing so, they make the same interactions with the minor groove of PKI as during decoding of tRNA (Ogle et al., 2001).
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fig3: Interaction of the CrPV-IRES with the Decoding Center of the 40S Subunit(A) Overview of the CrPV-IRES-ribosome.(B) Superposition of the CrPV-IRES with A, P, and E site tRNAs (from 2J00, Selmer et al., 2006), showing that the green pseudoknot PKI of the IRES is in the decoding center normally occupied by an A site tRNA anticodon stem loop.(C) Details of the interaction of PKI of the IRES showing that the three highly conserved 18S rRNA bases G577, A1755, and A1756 (corresponding to G530, A1492, and A1493 in E. coli) change conformation from relative to the structure of the empty yeast ribosome (purple; Ben-Shem et al., 2011). In doing so, they make the same interactions with the minor groove of PKI as during decoding of tRNA (Ogle et al., 2001).

Mentions: The CrPV-IRES spans all three tRNA binding sites of the ribosome (Figures 3A and 3B). PKI is inserted in the decoding center of the 40S ribosomal A site (Figures 3B and 3C). It is somewhat tilted toward the P site relative to A site tRNA (Figure 3B), thus more closely resembling a tRNA in the A/P hybrid state characteristic of a translocation intermediate. The interaction of PKI in the decoding center of the 40S subunit is very similar to that reported for normal decoding of tRNA in the A site (Ogle et al., 2001) and involves an interaction of the conserved 18S rRNA bases A1756 and A1755 (1493/92 in E. coli numbering) and G577 (530 in E. coli) with the minor groove of the elements that mimic the codon and anticodon in PKI. This shows that PKI mimics a decoding event in the A site.


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)

Interaction of the CrPV-IRES with the Decoding Center of the 40S Subunit(A) Overview of the CrPV-IRES-ribosome.(B) Superposition of the CrPV-IRES with A, P, and E site tRNAs (from 2J00, Selmer et al., 2006), showing that the green pseudoknot PKI of the IRES is in the decoding center normally occupied by an A site tRNA anticodon stem loop.(C) Details of the interaction of PKI of the IRES showing that the three highly conserved 18S rRNA bases G577, A1755, and A1756 (corresponding to G530, A1492, and A1493 in E. coli) change conformation from relative to the structure of the empty yeast ribosome (purple; Ben-Shem et al., 2011). In doing so, they make the same interactions with the minor groove of PKI as during decoding of tRNA (Ogle et al., 2001).
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

fig3: Interaction of the CrPV-IRES with the Decoding Center of the 40S Subunit(A) Overview of the CrPV-IRES-ribosome.(B) Superposition of the CrPV-IRES with A, P, and E site tRNAs (from 2J00, Selmer et al., 2006), showing that the green pseudoknot PKI of the IRES is in the decoding center normally occupied by an A site tRNA anticodon stem loop.(C) Details of the interaction of PKI of the IRES showing that the three highly conserved 18S rRNA bases G577, A1755, and A1756 (corresponding to G530, A1492, and A1493 in E. coli) change conformation from relative to the structure of the empty yeast ribosome (purple; Ben-Shem et al., 2011). In doing so, they make the same interactions with the minor groove of PKI as during decoding of tRNA (Ogle et al., 2001).
Mentions: The CrPV-IRES spans all three tRNA binding sites of the ribosome (Figures 3A and 3B). PKI is inserted in the decoding center of the 40S ribosomal A site (Figures 3B and 3C). It is somewhat tilted toward the P site relative to A site tRNA (Figure 3B), thus more closely resembling a tRNA in the A/P hybrid state characteristic of a translocation intermediate. The interaction of PKI in the decoding center of the 40S subunit is very similar to that reported for normal decoding of tRNA in the A site (Ogle et al., 2001) and involves an interaction of the conserved 18S rRNA bases A1756 and A1755 (1493/92 in E. coli numbering) and G577 (530 in E. coli) with the minor groove of the elements that mimic the codon and anticodon in PKI. This shows that PKI mimics a decoding event in the A site.

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