Structural basis for leucine-rich nuclear export signal recognition by CRM1

  • An Erratum to this article was published on 24 September 2009


CRM1 (also known as XPO1 and exportin 1) mediates nuclear export of hundreds of proteins through the recognition of the leucine-rich nuclear export signal (LR-NES). Here we present the 2.9 Å structure of CRM1 bound to snurportin 1 (SNUPN). Snurportin 1 binds CRM1 in a bipartite manner by means of an amino-terminal LR-NES and its nucleotide-binding domain. The LR-NES is a combined α-helical-extended structure that occupies a hydrophobic groove between two CRM1 outer helices. The LR-NES interface explains the consensus hydrophobic pattern, preference for intervening electronegative residues and inhibition by leptomycin B. The second nuclear export signal epitope is a basic surface on the snurportin 1 nucleotide-binding domain, which binds an acidic patch on CRM1 adjacent to the LR-NES site. Multipartite recognition of individually weak nuclear export signal epitopes may be common to CRM1 substrates, enhancing CRM1 binding beyond the generally low affinity LR-NES. Similar energetic construction is also used in multipartite nuclear localization signals to provide broad substrate specificity and rapid evolution in nuclear transport.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Overall structure of the CRM1–SNUPN complex.
Figure 2: The LR-NES-binding site.
Figure 3: Hydrophobic residues are critical for LR-NES recognition.
Figure 4: Localization of the SNUPN and its LR-NES in yeast.
Figure 5: Interactions of CRM1 with the SNUPN NES epitope II.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited in the Protein Data Bank under accession codes rcsb051649 and 3GB8.


  1. 1

    Tran, E. J., Bolger, T. A. & Wente, S. R. SnapShot: nuclear transport. Cell 131, 420 (2007)

  2. 2

    Weis, K. Regulating access to the genome: nucleocytoplasmic transport throughout the cell cycle. Cell 112, 441–451 (2003)

  3. 3

    Gorlich, D. & Kutay, U. Transport between the cell nucleus and the cytoplasm. Annu. Rev. Cell Dev. Biol. 15, 607–660 (1999)

  4. 4

    Conti, E. & Izaurralde, E. Nucleocytoplasmic transport enters the atomic age. Curr. Opin. Cell Biol. 13, 310–319 (2001)

  5. 5

    Dingwall, C., Sharnick, S. V. & Laskey, R. A. A polypeptide domain that specifies migration of nucleoplasmin into the nucleus. Cell 30, 449–458 (1982)

  6. 6

    Lanford, R. E. & Butel, J. S. Construction and characterization of an SV40 mutant defective in nuclear transport of T antigen. Cell 37, 801–813 (1984)

  7. 7

    Kalderon, D., Richardson, W. D., Markham, A. F. & Smith, A. E. Sequence requirements for nuclear location of simian virus 40 large-T antigen. Nature 311, 33–38 (1984)

  8. 8

    Lee, B. J. et al. Rules for nuclear localization sequence recognition by karyopherinβ2. Cell 126, 543–558 (2006)

  9. 9

    Wen, W., Meinkoth, J. L., Tsien, R. Y. & Taylor, S. S. Identification of a signal for rapid export of proteins from the nucleus. Cell 82, 463–473 (1995)

  10. 10

    Fischer, U. et al. The HIV-1 Rev activation domain is a nuclear export signal that accesses an export pathway used by specific cellular RNAs. Cell 82, 475–483 (1995)

  11. 11

    Richards, S. A., Carey, K. L. & Macara, I. G. Requirement of guanosine triphosphate-bound ran for signal-mediated nuclear protein export. Science 276, 1842–1844 (1997)

  12. 12

    Stade, K., Ford, C. S., Guthrie, C. & Weis, K. Exportin 1 (Crm1p) is an essential nuclear export factor. Cell 90, 1041–1050 (1997)

  13. 13

    Fornerod, M., Ohno, M., Yoshida, M. & Mattaj, I. W. CRM1 is an export receptor for leucine-rich nuclear export signals. Cell 90, 1051–1060 (1997)

  14. 14

    Ossareh-Nazari, B., Bachelerie, F. & Dargemont, C. Evidence for a role of CRM1 in signal-mediated nuclear protein export. Science 278, 141–144 (1997)

  15. 15

    Fukuda, M. et al. CRM1 is responsible for intracellular transport meditted by the nuclear export signal. Nature 390, 308–311 (1997)

  16. 16

    Neville, M. et al. The importin-β family member Crm1p bridges the interaction between Rev and the nuclear pore complex during nuclear export. Curr. Biol. 7, 767–775 (1997)

  17. 17

    Bogerd, H. P. et al. Protein sequence requirements for function of the human T-cell leukemia virus type 1 Rex nuclear export signal delineated by a novel in vivo randomization-selection assay. Mol. Cell. Biol. 16, 4207–4214 (1996)

  18. 18

    Henderson, B. R. & Eleftheriou, A. A comparison of the activity, sequence specificity, and CRM1-dependence of different nuclear export signals. Exp. Cell Res. 256, 213–224 (2000)

  19. 19

    la Cour, T. et al. Analysis and prediction of leucine-rich nuclear export signals. Protein Eng. Des. Sel. 17, 527–536 (2004)

  20. 20

    Kutay, U. & Guttinger, S. Leucine-rich nuclear-export signals: born to be weak. Trends Cell Biol. 15, 121–124 (2005)

  21. 21

    Engelsma, D., Bernad, R., Calafat, J. & Fornerod, M. Supraphysiological nuclear export signals bind CRM1 independently of RanGTP and arrest at Nup358. EMBO J. 23, 3643–3652 (2004)

  22. 22

    Cansizoglu, A. E. et al. Structure-based design of a pathway-specific nuclear import inhibitor. Nature Struct. Mol. Biol. 14, 452–454 (2007)

  23. 23

    Mancias, J. D. & Goldberg, J. Exiting the endoplasmic reticulum. Traffic 6, 278–285 (2005)

  24. 24

    Swanton, E. & High, S. ER targeting signals: more than meets the eye? Cell 127, 877–879 (2006)

  25. 25

    Kudo, N. et al. Leptomycin B inactivates CRM1/exportin 1 by covalent modification at a cysteine residue in the central conserved region. Proc. Natl Acad. Sci. USA 96, 9112–9117 (1999)

  26. 26

    Matsuyama, A. et al. ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe . Nature Biotechnol. 24, 841–847 (2006)

  27. 27

    Nishi, K. et al. Leptomycin B targets a regulatory cascade of crm1, a fission yeast nuclear protein, involved in control of higher order chromosome structure and gene expression. J. Biol. Chem. 269, 6320–6324 (1994)

  28. 28

    Paraskeva, E. et al. CRM1-mediated recycling of snurportin 1 to the cytoplasm. J. Cell Biol. 145, 255–264 (1999)

  29. 29

    Huber, J. et al. Snurportin1, an m3G-cap-specific nuclear import receptor with a novel domain structure. EMBO J. 17, 4114–4126 (1998)

  30. 30

    Petosa, C. et al. Architecture of CRM1/Exportin1 suggests how cooperativity is achieved during formation of a nuclear export complex. Mol. Cell 16, 761–775 (2004)

  31. 31

    Strasser, A., Dickmanns, A., Luhrmann, R. & Ficner, R. Structural basis for m3G-cap-mediated nuclear import of spliceosomal UsnRNPs by snurportin1. EMBO J. 24, 2235–2243 (2005)

  32. 32

    Mitrousis, G., Olia, A. S., Walker-Kopp, N. & Cingolani, G. Molecular basis for the recognition of snurportin 1 by importin beta. J. Biol. Chem. 283, 7877–7884 (2008)

  33. 33

    Dong, X., Biswas, A. & Chook, Y. M. Structural basis of assembly and disassembly of the CRM1 nuclear export complex. Nature Struct. Mol. Biol. 10.1038/nsmb.1585 (in the press)

  34. 34

    Suel, K. E., Cansizoglu, A. E. & Chook, Y. M. Atomic resolution structures in nuclear transport. Methods 39, 342–355 (2006)

  35. 35

    Matsuura, Y. & Stewart, M. Structural basis for the assembly of a nuclear export complex. Nature 432, 872–877 (2004)

  36. 36

    Jones, D. T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195–202 (1999)

  37. 37

    Meiler, J. & Baker, D. Coupled prediction of protein secondary and tertiary structure. Proc. Natl Acad. Sci. USA 100, 12105–12110 (2003)

  38. 38

    Askjaer, P. et al. The specificity of the CRM1-Rev nuclear export signal interaction is mediated by RanGTP. J. Biol. Chem. 273, 33414–33422 (1998)

  39. 39

    Thomas, F. & Kutay, U. Biogenesis and nuclear export of ribosomal subunits in higher eukaryotes depend on the CRM1 export pathway. J. Cell Sci. 116, 2409–2419 (2003)

  40. 40

    Kosugi, S., Hasebe, M., Tomita, M. & Yanagawa, H. Nuclear export signal consensus sequences defined using a localization-based yeast selection system. Traffic 9, 2053–2062 (2008)

  41. 41

    Englmeier, L. et al. RanBP3 influences interactions between CRM1 and its nuclear protein export substrates. EMBO Rep. 2, 926–932 (2001)

  42. 42

    Suel, K. E., Gu, H. & Chook, Y. M. Modular organization and combinatorial energetics of proline-tyrosine nuclear localization signals. PLoS Biol. 6, e137 (2008)

  43. 43

    Terwilliger, T. C. Maximum-likelihood density modification. Acta Crystallogr. D 56, 965–972 (2000)

  44. 44

    Terwilliger, T. C. & Berendzen, J. Automated MAD and MIR structure solution. Acta Crystallogr. D 55, 849–861 (1999)

  45. 45

    Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

  46. 46

    Sheldrick, G. M. A short history of SHELX. Acta Crystallogr. A 64, 112–122 (2008)

  47. 47

    Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

  48. 48

    Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

  49. 49

    Winn, M. D., Isupov, M. N. & Murshudov, G. N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D 57, 122–133 (2001)

  50. 50

    Sikorski, R. S. & Hieter, P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae . Genetics 122, 19–27 (1989)

Download references


We thank Y. Sheng, C. Kong, D. Tomchick and C. Dann for assistance during data collection and structure determination, S. Padrick for advice on fluorescence binding assays, G. Süel and T. Cagatay for help with microscopy, K. Weis for yeast strains and constructs, X. Zhang, L. Rice and M. Rosen for discussion. This work is funded by National Institute of Health (NIH) grants R01GM069909, R01GM069909-03S1, 5-T32-GM008297, Welch Foundation grant I-1532 and the UT Southwestern Endowed Scholars Program. Use of the Argonne National Laboratory Stuctural Biology Center beamlines at the Advanced Photon Source, was supported by the US Department of Energy, Office of Energy Research, under contract no. W-31-109-ENG-38.

Author information

Correspondence to Yuh Min Chook.

Supplementary information

Supplementary Information

This file contains Supplementary Table 1 and Supplementary Figures S1-S10 with Legends (PDF 1337 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Dong, X., Biswas, A., Süel, K. et al. Structural basis for leucine-rich nuclear export signal recognition by CRM1. Nature 458, 1136–1141 (2009).

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.