Structures of the tRNA export factor in the nuclear and cytosolic states

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Abstract

Transfer RNAs are among the most ubiquitous molecules in cells, central to decoding information from messenger RNAs on translating ribosomes. In eukaryotic cells, tRNAs are actively transported from their site of synthesis in the nucleus to their site of function in the cytosol. This is mediated by a dedicated nucleo-cytoplasmic transport factor of the karyopherin-β family (Xpot, also known as Los1 in Saccharomyces cerevisiae). Here we report the 3.2 Å resolution structure of Schizosaccharomyces pombe Xpot in complex with tRNA and RanGTP, and the 3.1 Å structure of unbound Xpot, revealing both nuclear and cytosolic snapshots of this transport factor. Xpot undergoes a large conformational change on binding cargo, wrapping around the tRNA and, in particular, binding to the tRNA 5′ and 3′ ends. The binding mode explains how Xpot can recognize all mature tRNAs in the cell and yet distinguish them from those that have not been properly processed, thus coupling tRNA export to quality control.

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Figure 1: Structure of the Xpot–RanGTP–tRNA complex.
Figure 2: The binding of RanGTP to Xpot.
Figure 3: Complementary tRNA-binding surfaces on Xpot.
Figure 4: Recognition of the tRNA 3′ and 5′ ends.
Figure 5: Conformational change of Xpot unbound and in complex.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structures have been deposited in the Protein Data Bank under accession codes 3IBV for Xpot and 3ICQ for the Xpot–RanGTP–tRNA complex.

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Acknowledgements

We would like to thank P. Brick for comments and critical reading of the manuscript. We also thank P. Reichelt and J. Ebert for technical assistance, S. Kuersten and I. Mattaj at the initial phase of the project, K. Valer-Saldana, S. Pleyer and J. Basquin of the MPI-Martinsried crystallization facility and the staff at the Swiss Light Source (Villigen, Switzerland) for assistance during data collection. We would like to thank C. Vonrhein (Global Phasing) for optimising the phase calculations of unbound Xpot with SHARP. This study was supported by the Max Planck Gesellschaft, the European Molecular Biology Laboratory (EMBL), the Sonderforschungsbereich SFB646 and the Gottfried Wilhelm Leibniz Program of the Deutsche Forschungsgemeinschaft (DFG), the EU grant 3D Repertoire contract number LSHG-CT-2005-512028.

Author Contributions N.F. identified S. pombe Xpot as the most promising orthologue for crystallisation, created the truncated tRNA construct and obtained initial, low-resolution crystals for the cargo-bound complex. M.J. crystallised unbound Xpot. A.G.C. solved the structure of unbound Xpot, obtained well-diffracting crystals of the ternary complex and solved its structure. E.C. supervised the project. A.G.C. and E.C. wrote the paper.

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Correspondence to Elena Conti.

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This file contains Supplementary Tables 1-2 and Supplementary Figures 1-10 with Legends and Supplementary References for Figure 8. (PDF 10586 kb)

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Cook, A., Fukuhara, N., Jinek, M. et al. Structures of the tRNA export factor in the nuclear and cytosolic states. Nature 461, 60–65 (2009) doi:10.1038/nature08394

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