Structure of Yeast Nuclear Pore Complexes

  • Lan Mi
  • Longfang Yao
  • Jiong MaEmail author
Part of the Nucleic Acids and Molecular Biology book series (NUCLEIC, volume 33)


Nuclear pore complexes (NPCs) are large protein complex assemblies by about 30 different proteins, called nucleoporins (Nups), embedded in the nuclear envelope. Most of transport of molecules between cytoplasm and nucleus occurs through the NPCs. The research of yeast and vertebrate NPC structure made big progress in the past decades. This chapter first reviews recent advances of NPC structure and architecture by electron microscopy and super-resolution and then further overviews the progress of NPC structure and dynamic in living yeast cells by a single molecular detection approach called single-point edge-excitation sub-diffraction (SPEED) microscopy. In the last section, we will discuss the perspective about the structure of yeast NPCs.



This work is supported by National Natural Science Foundation of China (61575046, 11574056, and 31500599) and Science and Technology Commission of Shanghai Municipality (Shanghai Rising-Star Program, 16QA1400400).


  1. Aitchison JD, Rout MP (2012) The yeast nuclear pore complex and transport through it. Genetics 190:855–883CrossRefPubMedPubMedCentralGoogle Scholar
  2. Aitchison JD, Rout MP, Marelli M, Blobel G, Wozniak RW (1995) 2 novel related yeast nucleoporins Nup170P and Nup157P – complementation with the vertebrate homolog Nup155P and functional interactions with the yeast nuclear pore-membrane protein POM152P. J Cell Biol 131:1133–1148CrossRefPubMedGoogle Scholar
  3. Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT et al (2007) Determining the architectures of macromolecular assemblies. Nature 450:683–694CrossRefPubMedGoogle Scholar
  4. Anderson TM, Clay MC, Cioffi AG, Diaz KA, Hisao GS, Tuttle MD, Nieuwkoop AJ, Comellas G, Maryum N, Wang S et al (2014) Amphotericin forms an extramembranous and fungicidal sterol sponge. Nat Chem Biol 10:400–406CrossRefPubMedPubMedCentralGoogle Scholar
  5. Brohawn SG, Partridge JR, Whittle JRR, Schwartz TU (2009) The nuclear pore complex has entered the atomic age. Structure 17:1156–1168CrossRefPubMedPubMedCentralGoogle Scholar
  6. Bui KH, von Appen A, DiGuilio AL, Ori A, Sparks L, Mackmull MT, Bock T, Hagen W, Andres-Pons A, Glavy JS et al (2013) Integrated structural analysis of the human nuclear pore complex scaffold. Cell 155:1233–1243CrossRefPubMedGoogle Scholar
  7. Chang HC, Kaiser CM, Hartl FU, Barral JM (2005) De novo folding of GFP fusion proteins: high efficiency in eukaryotes but not in bacteria. J Mol Biol 353:397–409CrossRefPubMedGoogle Scholar
  8. Cronshaw JA, Krutchinsky AN, Zhang WZ, Chait BT, Matunis MJ (2002) Proteomic analysis of the mammalian nuclear pore complex. J Cell Biol 158:915–927CrossRefPubMedPubMedCentralGoogle Scholar
  9. D’Angelo MA, Raices M, Panowski SH, Hetzer MW (2009) Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells. Cell 136:284–295CrossRefPubMedPubMedCentralGoogle Scholar
  10. de Lichtenberg U, Jensen LJ, Brunak S, Bork P (2005) Dynamic complex formation during the yeast cell cycle. Science 307:724–727CrossRefPubMedGoogle Scholar
  11. Fabre E, Hurt E (1997) Yeast genetics to dissect the nuclear pore complex and nucleocytoplasmic trafficking. Annu Rev Genet 31:277–313CrossRefPubMedGoogle Scholar
  12. Finan K, Raulf A, Heilemann M (2015) A set of homo-oligomeric standards allows accurate protein counting. Angew Chem Int Ed 54:12049–12052CrossRefGoogle Scholar
  13. Franke WW (1966) Isolated nuclear membranes. J Cell Biol 31:619–623CrossRefPubMedPubMedCentralGoogle Scholar
  14. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O’Shea EK, Weissman JS (2003) Global analysis of protein expression in yeast. Nature 425:737–741CrossRefPubMedGoogle Scholar
  15. Griffis ER, Altan N, Lippincott-Schwartz J, Powers MA (2002) Nup98 is a mobile nucleoporin with transcription-dependent dynamics. Mol Biol Cell 13:1282–1297CrossRefPubMedPubMedCentralGoogle Scholar
  16. Hinshaw JE, Milligan RA (2003) Nuclear pore complexes exceeding eightfold rotational symmetry. J Struct Biol 141:259–268CrossRefPubMedGoogle Scholar
  17. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK (2003) Global analysis of protein localization in budding yeast. Nature 425:686–691CrossRefPubMedGoogle Scholar
  18. Kopek BG, Shtengel G, Xu CS, Clayton DA, Hess HF (2012) Correlative 3D superresolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes. Proc Natl Acad Sci U S A 109:6136–6141CrossRefPubMedPubMedCentralGoogle Scholar
  19. Löschberger A, Svd L, Dabauvalle M-C, Rieger B, Heilemann M, Krohne G, Sauer M (2012) Super-resolution imaging visualizes the eightfold symmetry of gp210 proteins around the nuclear pore complex and resolves the central channel with nanometer resolution. J Cell Sci 125:570–575CrossRefPubMedGoogle Scholar
  20. Loschberger A, Franke C, Krohne G, van de Linde S, Sauer M (2014) Correlative super-resolution fluorescence and electron microscopy of the nuclear pore complex with molecular resolution. J Cell Sci 127:4351–4355CrossRefPubMedGoogle Scholar
  21. Ma J, Yang W (2010) Three-dimensional distribution of transient interactions in the nuclear pore complex obtained from single-molecule snapshots. Proc Natl Acad Sci USA 107:7305–7310CrossRefPubMedGoogle Scholar
  22. Mi L, Goryaynov A, Lindquist A, Rexach M, Yang WD (2015) Quantifying nucleoporin stoichiometry inside single nuclear pore complexes in vivo. Sci Rep 5:9372CrossRefPubMedPubMedCentralGoogle Scholar
  23. Nanguneri S, Flottmann B, Horstmann H, Heilemann M, Kuner T (2012) Three-dimensional, tomographic super-resolution fluorescence imaging of serially sectioned thick samples. Plos One 7:e38098CrossRefPubMedPubMedCentralGoogle Scholar
  24. Ori A, Banterle N, Iskar M, Andrés-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P et al (2013) Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines. Mol Syst Biol 9:648CrossRefPubMedPubMedCentralGoogle Scholar
  25. Pouwels LJ, Zhang L, Chan NH, Dorrestein PC, Wachter RM (2008) Kinetic isotope effect studies on the de novo rate of chromophore formation in fast- and slow-maturing GFP variants. Biochemistry 47:10111–10122CrossRefPubMedPubMedCentralGoogle Scholar
  26. Rabut G, Doye V, Ellenberg J (2004) Mapping the dynamic organization of the nuclear pore complex inside single living cells. Nat Cell Biol 6:1114–1121CrossRefPubMedGoogle Scholar
  27. Reichelt R, Holzenburg A, Buhle EL, Jarnik M, Engel A, Aebi U (1990) Correlation between structure and mass-distribution of the nuclear-pore complex and of distinct pore complex components. J Cell Biol 110:883–894CrossRefPubMedGoogle Scholar
  28. Rout MP, Blobel G (1993) Isolation of the yeast nuclear pore complex. J Cell Biol 123:771–783CrossRefPubMedGoogle Scholar
  29. Rout MP, Aitchison JD, Suprapto A, Hjertaas K, Zhao Y, Chait BT (2000) The yeast nuclear pore complex: composition, architecture, and transport mechanism. J Cell Biol 148:635–651CrossRefPubMedPubMedCentralGoogle Scholar
  30. Savas JN, Toyama BH, Xu T, Yates JR, Hetzer MW (2012) Extremely long-lived nuclear pore proteins in the rat brain. Science 335:942–942CrossRefPubMedPubMedCentralGoogle Scholar
  31. Strambio-De-Castillia C, Niepel M, Rout MP (2010) The nuclear pore complex: bridging nuclear transport and gene regulation. Nature Reviews Molecular Cell Biology 11:490–501CrossRefPubMedGoogle Scholar
  32. Stuwe T, Correia AR, Lin DH, Paduch M, Lu VT, Kossiakoff AA, Hoelz A (2015) Architecture of the nuclear pore complex coat. Science 347:1148–1152CrossRefPubMedPubMedCentralGoogle Scholar
  33. Suntharalingam M, Wente SR (2003) Peering through the pore: nuclear pore complex structure, assembly, and function. Developmental Cell 4:775–789CrossRefPubMedGoogle Scholar
  34. Szymborska A, de Marco A, Daigle N, Cordes VC, Briggs JAG, Ellenberg J (2013) Nuclear pore scaffold structure analyzed by super-resolution microscopy and particle averaging. Science 341:655–658CrossRefPubMedGoogle Scholar
  35. Tanudji M, Hevi S, Chuck SL (2002) Improperly folded green fluorescent protein is secreted via a non-classical pathway. J Cell Sci 115:3849–3857CrossRefPubMedGoogle Scholar
  36. Tie HC, Madugula V, Lu L (2016) The development of a single molecule fluorescence standard and its application in estimating the stoichiometry of the nuclear pore complex. Biochem Biophys Res Commun 478:1694–1699CrossRefPubMedGoogle Scholar
  37. von Appen A, Beck M (2016) Structure determination of the nuclear pore complex with three-dimensional cryo electron microscopy. J Mol Biol 428:2001–2010CrossRefGoogle Scholar
  38. von Appen A, Kosinski J, Sparks L, Ori A, DiGuilio AL, Vollmer B, Mackmull MT, Banterle N, Parca L, Kastritis P et al (2015) In situ structural analysis of the human nuclear pore complex. Nature 526:140CrossRefGoogle Scholar
  39. Wente SR, Blobel G (1994) Nup145 encodes a novel yeast glycine-leucine-phenylalanine-glycine (GLFG) nucleoporin required for nuclear-envelope structure. Journal Of Cell Biology 125:955–969CrossRefPubMedGoogle Scholar
  40. Yang Q, Rout MP, Akey CW (1998) Three-dimensional architecture of the Isolated yeast nuclear pore complex: functional and evolutionary implications. Mol Cell 1:223–234CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Optical Science and EngineeringShanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan UniversityShanghaiChina

Personalised recommendations