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Following the signal sequence from ribosomal tunnel exit to signal recognition particle

Abstract

Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane1. This process is dependent on signal sequence recognition on the ribosome by the signal recognition particle (SRP), which results in targeting of the ribosome–nascent-chain complex to the protein-conducting channel at the membrane2,3. Here we present an ensemble of structures at subnanometre resolution, revealing the signal sequence both at the ribosomal tunnel exit and in the bacterial and eukaryotic ribosome–SRP complexes. Molecular details of signal sequence interaction in both prokaryotic and eukaryotic complexes were obtained by fitting high-resolution molecular models. The signal sequence is presented at the ribosomal tunnel exit in an exposed position ready for accommodation in the hydrophobic groove of the rearranged SRP54 M domain. Upon ribosome binding, the SRP54 NG domain also undergoes a conformational rearrangement, priming it for the subsequent docking reaction with the NG domain of the SRP receptor. These findings provide the structural basis for improving our understanding of the early steps of co-translational protein sorting.

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Figure 1: Cryo-electron microscopic structure of programmed 70S ribosome (RNC) with signal sequence.
Figure 2: Structure of E. coli 70S RNC–SRP complex.
Figure 3: Transfer of signal sequence from the ribosome to SRP.
Figure 4: Mammalian SRP bound to 80S RNC.

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Acknowledgements

This work was supported by grants from the VolkswagenStiftung and the Deutsche Forschungsgemeinschaft SFB594 (to R.B.) and SFB638 (to I.S.) and by the European Union and Senatsverwaltung für Wissenschaft, Forschung und Kultur Berlin (UltraStructureNetwork).

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Correspondence to Roland Beckmann.

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Competing interests

Coordinates of the atomic models of SRP have been deposited in the PDB under accession numbers 2j28 and 2j37. The cryo-electron microscopic maps have been deposited in the 3D-EM database under accession numbers EMD1261 (E. coli SRP–RNC), EMD1263 (E. coli RNC) and EMD1264 (mammalian SRP-RNC). Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Methods

Methods section describing programming, purification and reconstitution of ribosomal complexes, followed by description of structure determination by cryo-EM and single particle analysis. This file also contains Supplementary Table 1. (DOC 42 kb)

Supplementary Figure 1

Alignment of the C-terminus of the mammalian SRP54 M domain with secondary structure prediction and usage in model. (JPG 33 kb)

Supplementary Figure Legend

Text to accompany Supplementary Figure 1. Sequence and secondary structure prediction of C-terminal domain of mammalian (Canis familiaris) SRP54 (DOC 24 kb)

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Halic, M., Blau, M., Becker, T. et al. Following the signal sequence from ribosomal tunnel exit to signal recognition particle. Nature 444, 507–511 (2006). https://doi.org/10.1038/nature05326

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