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

doi:10.1016/j.cell.2021.12.015

Comprehensive structure and functional adaptations of the yeast nuclear pore complex

Cell. 2022 Jan 20;185(2):361-378.e25. doi: 10.1016/j.cell.2021.12.015. Epub 2022 Jan 3.

Authors

Christopher W Akey¹, Digvijay Singh², Christna Ouch³, Ignacia Echeverria⁴, Ilona Nudelman⁵, Joseph M Varberg⁶, Zulin Yu⁶, Fei Fang⁷, Yi Shi⁷, Junjie Wang⁸, Daniel Salzberg⁹, Kangkang Song¹⁰, Chen Xu¹⁰, James C Gumbart¹¹, Sergey Suslov², Jay Unruh⁶, Sue L Jaspersen¹², Brian T Chait⁸, Andrej Sali¹³, Javier Fernandez-Martinez¹⁴, Steven J Ludtke¹⁵, Elizabeth Villa¹⁶, Michael P Rout¹⁷

Affiliations

¹ Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA. Electronic address: cakey@bu.edu.
² Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
³ Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
⁴ Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, San Francisco, San Francisco, CA 94158, USA.
⁵ Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
⁶ Stowers Institute for Medical Research, Kansas City, MO, USA.
⁷ Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA.
⁸ Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA.
⁹ Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
¹⁰ Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
¹¹ School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA.
¹² Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA.
¹³ Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
¹⁴ Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: jfernandez@rockefeller.edu.
¹⁵ Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA. Electronic address: sludtke@bcm.edu.
¹⁶ Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: evilla@ucsd.edu.
¹⁷ Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: rout@rockefeller.edu.

Abstract

Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub-nanometer resolution to show how flexible connectors tie together different structural and functional layers. These connectors may be targets for phosphorylation and regulated disassembly in cells with an open mitosis. Moreover, some nucleoporin pairs and transport factors have similar interaction motifs, which suggests an evolutionary and mechanistic link between assembly and transport. We provide evidence for three major NPC variants that may foreshadow functional specializations at the nuclear periphery. Cryo-electron tomography extended these studies, providing a model of the in situ NPC with a radially expanded inner ring. Our comprehensive model reveals features of the nuclear basket and central transporter, suggests a role for the lumenal Pom152 ring in restricting dilation, and highlights structural plasticity that may be required for transport.

Keywords: NPC evolution; Nuclear pore complex; cryo-electron microscopy; cryo-electron tomography; inner ring dilation; nuclear basket; nucleocytoplasmic transport; nucleoporins; structural isoforms.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Adaptation, Physiological*
Amino Acid Motifs
Amino Acid Sequence
Fluorescence
Molecular Docking Simulation
Nuclear Envelope / metabolism
Nuclear Pore / chemistry
Nuclear Pore / metabolism*
Nuclear Pore Complex Proteins / chemistry
Nuclear Pore Complex Proteins / metabolism
Protein Domains
Reproducibility of Results
Saccharomyces cerevisiae / physiology*
Saccharomyces cerevisiae Proteins / chemistry
Saccharomyces cerevisiae Proteins / metabolism

Substances

Nuclear Pore Complex Proteins
Saccharomyces cerevisiae Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding