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Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB


Accurate translation of genetic information into protein sequence depends on complete messenger RNA molecules. Truncated mRNAs cause synthesis of defective proteins, and arrest ribosomes at the end of their incomplete message. In bacteria, a hybrid RNA molecule that combines the functions of both transfer and messenger RNAs (called tmRNA) rescues stalled ribosomes, and targets aberrant, partially synthesized, proteins for proteolytic degradation1,2. Here we report the 3.2-Å-resolution structure of the tRNA-like domain of tmRNA (tmRNAΔ) in complex with small protein B (SmpB), a protein essential for biological functions of tmRNA. We find that the flexible RNA molecule adopts an open L-shaped conformation and SmpB binds to its elbow region, stabilizing the single-stranded D-loop in an extended conformation. The most striking feature of the structure of tmRNAΔ is a 90° rotation of the TΨC-arm around the helical axis. Owing to this unusual conformation, the SmpB–tmRNAΔ complex positioned into the A-site of the ribosome orients SmpB towards the small ribosomal subunit, and directs tmRNA towards the elongation-factor binding region of the ribosome. On the basis of this structure, we propose a model for the binding of tmRNA on the ribosome.

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Figure 1: Overview of the SmpB–tmRNAΔ structure.
Figure 2: Two views of tmRNAΔ in comparison with tRNAPhe (ref. 14).
Figure 3: SmpB–tmRNAΔ interactions.
Figure 4: Model of the interactions between the SmpB–tmRNAΔ complex and the ribosome.


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We thank C. Schulze-Briese, T. Tomizaki and A. Wagner (SLS, Villigen) D. Sargent, and the team at Swiss Norwegian Beamline (ESRF, Grenoble) for assistance in data collection, V. Ramakrishnan for comments on the manuscript, and D. Goven for help in the footprint assays. P.W.H. is supported by an EMBO fellowship. This work was supported by the Swiss National Science Foundation (SNSF), the NCCR Structural Biology programme of the SNSF, and a Young Investigator grant from the Human Frontier Science Program.

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Correspondence to Nenad Ban.

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Supplementary information


Supplementary Figure 1: Chemical and enzymatic footprints of tmRNAΔ as free molecule and in complex with SmpB. (JPG 135 kb)

Supplementary Figure Legend (DOC 20 kb)

Supplementary Table 1: containing data collection, phasing and refinement statistics. (DOC 26 kb)

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Gutmann, S., Haebel, P., Metzinger, L. et al. Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB. Nature 424, 699–703 (2003).

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