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A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure

Author

Listed:
  • Sarah A. Nordeen

    (Massachusetts Institute of Technology)

  • Kasper R. Andersen

    (Massachusetts Institute of Technology)

  • Kevin E. Knockenhauer

    (Massachusetts Institute of Technology)

  • Jessica R. Ingram

    (Boston Children’s Hospital and Harvard Medical School)

  • Hidde L. Ploegh

    (Boston Children’s Hospital and Harvard Medical School)

  • Thomas U. Schwartz

    (Massachusetts Institute of Technology)

Abstract

Nuclear pore complexes (NPCs) are the main conduits for molecular exchange across the nuclear envelope. The NPC is a modular assembly of ~500 individual proteins, called nucleoporins or nups. Most scaffolding nups are organized in two multimeric subcomplexes, the Nup84 or Y complex and the Nic96 or inner ring complex. Working in S. cerevisiae, and to study the assembly of these two essential subcomplexes, we here develop a set of twelve nanobodies that recognize seven constituent nucleoporins of the Y and Nic96 complexes. These nanobodies all bind specifically and with high affinity. We present structures of several nup-nanobody complexes, revealing their binding sites. Additionally, constitutive expression of the nanobody suite in S. cerevisiae detect accessible and obstructed surfaces of the Y complex and Nic96 within the NPC. Overall, this suite of nanobodies provides a unique and versatile toolkit for the study of the NPC.

Suggested Citation

  • Sarah A. Nordeen & Kasper R. Andersen & Kevin E. Knockenhauer & Jessica R. Ingram & Hidde L. Ploegh & Thomas U. Schwartz, 2020. "A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19884-6
    DOI: 10.1038/s41467-020-19884-6
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