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Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex

View ORCID ProfileChristopher W. Akey, View ORCID ProfileDigvijay Singh, View ORCID ProfileChristna Ouch, View ORCID ProfileIgnacia Echeverria, View ORCID ProfileIlona Nudelman, View ORCID ProfileJoseph M Varberg, Zulin Yu, View ORCID ProfileFei Fang, View ORCID ProfileYi Shi, Junjie Wang, View ORCID ProfileDaniel Salzberg, Kangkang Song, Chen Xu, View ORCID ProfileJames C. Gumbart, View ORCID ProfileSergey Suslov, View ORCID ProfileJay Unruh, View ORCID ProfileSue L Jaspersen, View ORCID ProfileBrian T. Chait, View ORCID ProfileAndrej Sali, View ORCID ProfileJavier Fernandez-Martinez, View ORCID ProfileSteven J. Ludtke, View ORCID ProfileElizabeth Villa, View ORCID ProfileMichael P. Rout
doi: https://doi.org/10.1101/2021.10.29.466335
Christopher W. Akey
1Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118, USA
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  • For correspondence: cakey@bu.edu jfernandez@rockefeller.edu sludtke@bcm.edu evilla@ucsd.edu rout@rockefeller.edu
Digvijay Singh
2Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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Christna Ouch
1Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118, USA
3Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605
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Ignacia Echeverria
4Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
12Department of Cellular and Molecular Pharmacology, San Francisco, San Francisco, CA 94158, USA
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Ilona Nudelman
5Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA
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Joseph M Varberg
9Stowers Institute for Medical Research, Kansas City, MO, USA
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Zulin Yu
9Stowers Institute for Medical Research, Kansas City, MO, USA
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Fei Fang
6Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
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Yi Shi
6Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
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Junjie Wang
7Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
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Daniel Salzberg
4Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
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Kangkang Song
3Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605
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Chen Xu
3Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605
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James C. Gumbart
8School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Sergey Suslov
2Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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Jay Unruh
9Stowers Institute for Medical Research, Kansas City, MO, USA
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Sue L Jaspersen
9Stowers Institute for Medical Research, Kansas City, MO, USA
10Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
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Brian T. Chait
7Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
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Andrej Sali
4Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
13Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
14Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
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Javier Fernandez-Martinez
5Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA
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  • For correspondence: cakey@bu.edu jfernandez@rockefeller.edu sludtke@bcm.edu evilla@ucsd.edu rout@rockefeller.edu
Steven J. Ludtke
11Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA
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  • For correspondence: cakey@bu.edu jfernandez@rockefeller.edu sludtke@bcm.edu evilla@ucsd.edu rout@rockefeller.edu
Elizabeth Villa
2Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
15Howard Hughes Medical Institute, University of California San Diego
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  • For correspondence: cakey@bu.edu jfernandez@rockefeller.edu sludtke@bcm.edu evilla@ucsd.edu rout@rockefeller.edu
Michael P. Rout
5Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA
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  • ORCID record for Michael P. Rout
  • For correspondence: cakey@bu.edu jfernandez@rockefeller.edu sludtke@bcm.edu evilla@ucsd.edu rout@rockefeller.edu
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Abstract

Nuclear Pore Complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the yeast NPC in which the inner ring is resolved by cryo-EM at - helical resolution to show how flexible connectors tie together different structural and functional layers in the spoke. These connectors are targets for phosphorylation and regulated disassembly in cells with an open mitosis. Moreover, some nucleoporin pairs and karyopherins have similar interaction motifs, which suggests an evolutionary and mechanistic link between assembly and transport. We also provide evidence for three major NPC variants that foreshadow functional specializations at the nuclear periphery. Cryo-electron tomography extended these studies to provide a comprehensive model of the in situ NPC with a radially-expanded inner ring. Our model reveals novel features of the central transporter and nuclear basket, suggests a role for the lumenal ring in restricting dilation and highlights the structural plasticity required for transport by the NPC.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • We added a schematic figure to show our discoveries, other minor rearrangements.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 03, 2021.
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Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex
Christopher W. Akey, Digvijay Singh, Christna Ouch, Ignacia Echeverria, Ilona Nudelman, Joseph M Varberg, Zulin Yu, Fei Fang, Yi Shi, Junjie Wang, Daniel Salzberg, Kangkang Song, Chen Xu, James C. Gumbart, Sergey Suslov, Jay Unruh, Sue L Jaspersen, Brian T. Chait, Andrej Sali, Javier Fernandez-Martinez, Steven J. Ludtke, Elizabeth Villa, Michael P. Rout
bioRxiv 2021.10.29.466335; doi: https://doi.org/10.1101/2021.10.29.466335
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Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex
Christopher W. Akey, Digvijay Singh, Christna Ouch, Ignacia Echeverria, Ilona Nudelman, Joseph M Varberg, Zulin Yu, Fei Fang, Yi Shi, Junjie Wang, Daniel Salzberg, Kangkang Song, Chen Xu, James C. Gumbart, Sergey Suslov, Jay Unruh, Sue L Jaspersen, Brian T. Chait, Andrej Sali, Javier Fernandez-Martinez, Steven J. Ludtke, Elizabeth Villa, Michael P. Rout
bioRxiv 2021.10.29.466335; doi: https://doi.org/10.1101/2021.10.29.466335

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