Structure and gating of the nuclear pore complex
10.1038/ncomms8532
Crossref journal-article
Springer Science and Business Media LLC
Nature Communications (297)
Abstract

AbstractNuclear pore complexes (NPCs) perforate the nuclear envelope and allow the exchange of macromolecules between the nucleus and the cytoplasm. To acquire a deeper understanding of this transport mechanism, we analyse the structure of the NPC scaffold and permeability barrier, by reconstructing the Xenopus laevis oocyte NPC from native nuclear envelopes up to 20 Å resolution by cryo-electron tomography in conjunction with subtomogram averaging. In addition to resolving individual protein domains of the NPC constituents, we propose a model for the architecture of the molecular gate at its central channel. Furthermore, we compare and contrast this native NPC structure to one that exhibits reduced transport activity and unveil the spatial properties of the NPC gate.

Bibliography

Eibauer, M., Pellanda, M., Turgay, Y., Dubrovsky, A., Wild, A., & Medalia, O. (2015). Structure and gating of the nuclear pore complex. Nature Communications, 6(1).

Authors 6
  1. Matthias Eibauer (first)
  2. Mauro Pellanda (additional)
  3. Yagmur Turgay (additional)
  4. Anna Dubrovsky (additional)
  5. Annik Wild (additional)
  6. Ohad Medalia (additional)
References 49 Referenced 176
  1. Brohawn, S. G., Partridge, J. R., Whittle, J. R. R. & Schwartz, T. U. The nuclear pore complex has entered the atomic age. Structure 17, 1156–1168 (2009). (10.1016/j.str.2009.07.014) / Structure by SG Brohawn (2009)
  2. Hoelz, A., Debler, E. W. & Blobel, G. The structure of the nuclear pore complex. Annu. Rev. Biochem. 80, 613–643 (2011). (10.1146/annurev-biochem-060109-151030) / Annu. Rev. Biochem. by A Hoelz (2011)
  3. Reichelt, R. et al. Correlation between structure and mass distribution of the nuclear pore complex and of distinct pore complex components. J. Cell Biol. 110, 883–894 (1990). (10.1083/jcb.110.4.883) / J. Cell Biol. by R Reichelt (1990)
  4. Cronshaw, J. M., Krutchinsky, A. N., Zhang, W., Chait, B. T. & Matunis, M. J. Proteomic analysis of the mammalian nuclear pore complex. J. Cell Biol. 158, 915–927 (2002). (10.1083/jcb.200206106) / J. Cell Biol. by JM Cronshaw (2002)
  5. Mohr, D., Frey, S., Fischer, T., Guettler, T. & Goerlich, D. Characterization of the passive permeability barrier of nuclear pore complexes. EMBO J. 28, 2541–2553 (2009). (10.1038/emboj.2009.200) / EMBO J. by D Mohr (2009)
  6. Fried, H. & Kutay, U. Nucleocytoplasmic transport: taking an inventory. Cell. Mol. Life Sci. 60, 1659–1688 (2003). (10.1007/s00018-003-3070-3) / Cell. Mol. Life Sci. by H Fried (2003)
  7. Rexach, M. & Blobel, G. Protein import into nuclei: association and dissociation reactions involving transport substrate, transport factors, and nucleoporins. Cell 83, 683–692 (1995). (10.1016/0092-8674(95)90181-7) / Cell by M Rexach (1995)
  8. Pante, N. & Kann, M. Nuclear pore complex is able to transport macromolecules with diameters of ∼39 nm. Mol. Biol. Cell 13, 425–434 (2002). (10.1091/mbc.01-06-0308) / Mol. Biol. Cell by N Pante (2002)
  9. Akey, C. W. & Radermacher, M. Architecture of the Xenopus nuclear pore complex revealed by three-dimensional cryo-electron microscopy. J. Cell Biol. 122, 1–19 (1993). (10.1083/jcb.122.1.1) / J. Cell Biol. by CW Akey (1993)
  10. Beck, M. et al. Nuclear pore complex structure and dynamics revealed by cryoelectron tomography. Science 306, 1387–1390 (2004). (10.1126/science.1104808) / Science by M Beck (2004)
  11. Beck, M., Lucic, V., Foerster, F., Baumeister, W. & Medalia, O. Snapshots of nuclear pore complexes in action captured by cryo-electron tomography. Nature 449, 611–615 (2007). (10.1038/nature06170) / Nature by M Beck (2007)
  12. Frenkiel-Krispin, D., Maco, B., Aebi, U. & Medalia, O. Structural analysis of a metazoan nuclear pore complex reveals a fused concentric ring architecture. J. Mol. Biol. 395, 578–586 (2010). (10.1016/j.jmb.2009.11.010) / J. Mol. Biol. by D Frenkiel-Krispin (2010)
  13. Maimon, T., Elad, N., Dahan, I. & Medalia, O. The human nuclear pore complex as revealed by cryo-electron tomography. Structure 20, 998–1006 (2012). (10.1016/j.str.2012.03.025) / Structure by T Maimon (2012)
  14. Bui, K. H. et al. Integrated structural analysis of the human nuclear pore complex scaffold. Cell 155, 1233–1243 (2013). (10.1016/j.cell.2013.10.055) / Cell by KH Bui (2013)
  15. Lutzmann, M., Kunze, R., Buerer, A., Aebi, U. & Hurt, E. Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins. EMBO J. 21, 387–397 (2002). (10.1093/emboj/21.3.387) / EMBO J. by M Lutzmann (2002)
  16. Kampmann, M., Atkinson, C. E., Mattheyses, A. L. & Simon, S. M. Mapping the orientation of nuclear pore proteins in living cells with polarized fluorescence microscopy. Nat. Struct. Biol. 18, 643–649 (2011). (10.1038/nsmb.2056) / Nat. Struct. Biol. by M Kampmann (2011)
  17. Szymborska, A. et al. Nuclear pore scaffold structure analysed by super-resolution microscopy and particle averaging. Science 341, 655–658 (2013). (10.1126/science.1240672) / Science by A Szymborska (2013)
  18. Walther, T. C. et al. The conserved Nup107-160 complex is critical for nuclear pore complex assembly. Cell 113, 195–206 (2003). (10.1016/S0092-8674(03)00235-6) / Cell by TC Walther (2003)
  19. Harel, A. et al. Removal of a single pore subcomplex results in vertebrate nuclei devoid of nuclear pores. Mol. Cell 11, 853–864 (2003). (10.1016/S1097-2765(03)00116-3) / Mol. Cell by A Harel (2003)
  20. Rout, M. P. et al. The yeast nuclear pore complex: composition, architecture, and transport mechanism. J. Cell Biol. 148, 635–651 (2000). (10.1083/jcb.148.4.635) / J. Cell Biol. by MP Rout (2000)
  21. Denning, D. P., Patel, S. S., Uversky, V., Fink, A. L. & Rexach, M. Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded. Proc. Natl Acad. Sci. USA 100, 2450–2455 (2003). (10.1073/pnas.0437902100) / Proc. Natl Acad. Sci. USA by DP Denning (2003)
  22. Lucic, V., Foerster, F. & Baumeister, W. Structural studies by electron tomography: from cells to molecules. Annu. Rev. Biochem. 74, 833–865 (2005). (10.1146/annurev.biochem.73.011303.074112) / Annu. Rev. Biochem. by V Lucic (2005)
  23. Dubochet, J. et al. Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys. 21, 129–228 (1988). (10.1017/S0033583500004297) / Q. Rev. Biophys. by J Dubochet (1988)
  24. Eibauer, M. et al. Unraveling the structure of membrane proteins in situ by transfer function corrected cryo-electron tomography. J. Struct. Biol. 180, 488–496 (2012). (10.1016/j.jsb.2012.09.008) / J. Struct. Biol. by M Eibauer (2012)
  25. Alber, F. et al. The molecular architecture of the nuclear pore complex. Nature 450, 695–701 (2007). (10.1038/nature06405) / Nature by F Alber (2007)
  26. Stoffler, D. et al. Cryo-electron tomography provides novel insights into nuclear pore architecture: Implications for nucleocytoplasmic transport. J. Mol. Biol. 328, 119–130 (2003). (10.1016/S0022-2836(03)00266-3) / J. Mol. Biol. by D Stoffler (2003)
  27. Gaik, M. et al. Structural basis for assembly and function of the Nup82 complex in the nuclear pore scaffold. J. Cell Biol. 208, 283–297 (2015). (10.1083/jcb.201411003) / J. Cell Biol. by M Gaik (2015)
  28. Yamada, J. et al. A bimodal distribution of two distinct categories of intrinsically disordered structures with separate functions in FG nucleoporins. Mol. Cell. Proteomics 9, 2205–2224 (2010). (10.1074/mcp.M000035-MCP201) / Mol. Cell. Proteomics by J Yamada (2010)
  29. Ries, J., Kaplan, C., Platonova, E., Eghlidi, H. & Ewers, H. A simple, versatile method for GFP-based super-resolution microscopy via nanobodies. Nat. Methods 9, 582–584 (2012). (10.1038/nmeth.1991) / Nat. Methods by J Ries (2012)
  30. Beck, F. et al. Near-atomic resolution structural model of the yeast 26S proteasome. Proc. Natl Acad. Sci. USA 109, 14870–14875 (2012). (10.1073/pnas.1213333109) / Proc. Natl Acad. Sci. USA by F Beck (2012)
  31. Scheres, S. H. W. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012). (10.1038/nmeth.2115) / Nat. Methods by SHW Scheres (2012)
  32. Robinson, C. V., Sali, A. & Baumeister, W. The molecular sociology of the cell. Nature 450, 973–982 (2007). (10.1038/nature06523) / Nature by CV Robinson (2007)
  33. Kampmann, M. & Blobel, G. Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex. Nat. Struct. Biol. 16, 782–788 (2009). (10.1038/nsmb.1618) / Nat. Struct. Biol. by M Kampmann (2009)
  34. Patel, S. S., Belmont, B. J., Sante, J. M. & Rexach, M. F. Natively unfolded nucleoporins gate protein diffusion across the nuclear pore complex. Cell 129, 83–96 (2007). (10.1016/j.cell.2007.01.044) / Cell by SS Patel (2007)
  35. Milles, S. et al. Facilitated aggregation of FG nucleoporins under molecular crowding conditions. EMBO Rep. 14, 178–183 (2013). (10.1038/embor.2012.204) / EMBO Rep. by S Milles (2013)
  36. Estroff, L. A., Leiserowitz, L., Addadi, L., Weiner, S. & Hamilton, A. D. Characterization of an organic hydrogel: A cryo-transmission electron microscopy and x-ray diffraction study. Adv. Mater. 15, 38–42 (2003). (10.1002/adma.200390004) / Adv. Mater. by LA Estroff (2003)
  37. Frey, S. & Goerlich, D. A saturated FG-repeat hydrogel can reproduce the permeability properties of nuclear pore complexes. Cell 130, 512–523 (2007). (10.1016/j.cell.2007.06.024) / Cell by S Frey (2007)
  38. Lim, R. Y. H. et al. Nanomechanical basis of selective gating by the nuclear pore complex. Science 318, 640–643 (2007). (10.1126/science.1145980) / Science by RYH Lim (2007)
  39. Jarnik, M. & Aebi, U. Toward a more complete 3-D structure of the nuclear pore complex. J. Struct. Biol. 107, 291–308 (1991). (10.1016/1047-8477(91)90054-Z) / J. Struct. Biol. by M Jarnik (1991)
  40. Stick, R. & Goldberg, M. W. Oocytes as an experimental system to analyse the ultrastructure of endogenous and ectopically expressed nuclear envelope components by field-emission scanning electron microscopy. Methods 51, 170–176 (2010). (10.1016/j.ymeth.2010.01.015) / Methods by R Stick (2010)
  41. Fernandez, J. J., Li, S. & Crowther, R. A. CTF determination and correction in electron cryotomography. Ultramicroscopy 106, 587–596 (2006). (10.1016/j.ultramic.2006.02.004) / Ultramicroscopy by JJ Fernandez (2006)
  42. Zanetti, G., Riches, J. D., Fuller, S. D. & Briggs, J. A. G. Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging. J. Struct. Biol. 168, 305–312 (2009). (10.1016/j.jsb.2009.08.002) / J. Struct. Biol. by G Zanetti (2009)
  43. Nickell, S. et al. TOM software toolbox: acquisition and analysis for electron tomography. J. Struct. Biol. 149, 227–234 (2005). (10.1016/j.jsb.2004.10.006) / J. Struct. Biol. by S Nickell (2005)
  44. Foerster, F., Medalia, O., Zauberman, N., Baumeister, W. & Fass, D. Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography. Proc. Natl Acad. Sci. USA 102, 4729–4734 (2005). (10.1073/pnas.0409178102) / Proc. Natl Acad. Sci. USA by F Foerster (2005)
  45. Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). (10.1002/jcc.20084) / J. Comput. Chem. by EF Pettersen (2004)
  46. Bilokapic, S. & Schwartz, T. U. Molecular basis for Nup37 and ELY5/ELYS recruitment to the nuclear pore complex. Proc. Natl Acad. Sci. USA 109, 15241–15246 (2012). (10.1073/pnas.1205151109) / Proc. Natl Acad. Sci. USA by S Bilokapic (2012)
  47. Brohawn, S. G. & Schwartz, T. U. Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice. Nat. Struct. Biol. 16, 1173–1177 (2009). (10.1038/nsmb.1713) / Nat. Struct. Biol. by SG Brohawn (2009)
  48. Brohawn, S. G., Leksa, N. C., Spear, E. D., Rajashankar, K. R. & Schwartz, T. U. Structural evidence for common ancestry of the nuclear pore complex and vesicle coats. Science 322, 1369–1373 (2008). (10.1126/science.1165886) / Science by SG Brohawn (2008)
  49. Van Heel, M. & Schatz, M. Fourier shell correlation threshold criteria. J. Struct. Biol. 151, 250–262 (2005). (10.1016/j.jsb.2005.05.009) / J. Struct. Biol. by M Van Heel (2005)
Dates
Type When
Created 10 years, 1 month ago (June 26, 2015, 7:42 a.m.)
Deposited 2 years, 7 months ago (Jan. 5, 2023, 6:23 a.m.)
Indexed 3 days, 10 hours ago (Aug. 21, 2025, 12:53 p.m.)
Issued 10 years, 1 month ago (June 26, 2015)
Published 10 years, 1 month ago (June 26, 2015)
Published Online 10 years, 1 month ago (June 26, 2015)
Funders 0

None

@article{Eibauer_2015, title={Structure and gating of the nuclear pore complex}, volume={6}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/ncomms8532}, DOI={10.1038/ncomms8532}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Eibauer, Matthias and Pellanda, Mauro and Turgay, Yagmur and Dubrovsky, Anna and Wild, Annik and Medalia, Ohad}, year={2015}, month=jun }