Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif

Nordeen, Sarah A.; Turman, Daniel L.; Schwartz, Thomas U.

doi:10.1038/s41467-020-19885-5

Title: Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif

Journal Article · Fri Nov 27 00:00:00 EST 2020 · Nature Communications

DOI:https://doi.org/10.1038/s41467-020-19885-5· OSTI ID:1729714

^[1]; Turman, Daniel L. ^[1];

^[1]

Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

The hallmark of the eukaryotic cell is the complex endomembrane system that compartmentalizes cellular functions. Transport into and out of the nucleus occurs through the nuclear pore complex (NPC). The heptameric Nup84 or Y complex is an essential scaffolding component of the NPC. Here we report two nanobody-bound structures: the full-length Nup84-Nup133 C-terminal domain complex and the Nup133 N-terminal domain, both from S. cerevisiae. Together with previously published structures, this work enables the structural description of the entire 575 kDa Y complex from one species. The structure of Nup84-Nup133CTD details the high flexibility of this dimeric unit of the Y complex. Further, the Nup133NTD contains a structurally conserved amphipathic lipid packing sensor motif, confirmed by liposome interaction studies. The presented structures reveal important details about the function of the Y complex that affect our understanding of NPC structure and assembly.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE

Contributing Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1729714

Journal Information:: Nature Communications, Vol. 11, Issue 1; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (75)

Integrative structure and functional anatomy of a nuclear pore complex Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona Nature, Vol. 555, Issue 7697 https://doi.org/10.1038/nature26003	journal	March 2018
A general amphipathic α-helical motif for sensing membrane curvature Drin, Guillaume; Casella, Jean-François; Gautier, Romain Nature Structural & Molecular Biology, Vol. 14, Issue 2 https://doi.org/10.1038/nsmb1194	journal	January 2007
Cell type‐specific nuclear pores: a case in point for context‐dependent stoichiometry of molecular machines Ori, Alessandro; Banterle, Niccolò; Iskar, Murat Molecular Systems Biology, Vol. 9, Issue 1 https://doi.org/10.1038/msb.2013.4	journal	January 2013
Structure and gating of the nuclear pore complex Eibauer, Matthias; Pellanda, Mauro; Turgay, Yagmur Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms8532	journal	June 2015
Allosteric activation of apicomplexan calcium-dependent protein kinases Ingram, Jessica R.; Knockenhauer, Kevin E.; Markus, Benedikt M. Proceedings of the National Academy of Sciences, Vol. 112, Issue 36 https://doi.org/10.1073/pnas.1505914112	journal	August 2015
Molecular architecture of the inner ring scaffold of the human nuclear pore complex Kosinski, J.; Mosalaganti, S.; von Appen, A. Science, Vol. 352, Issue 6283 https://doi.org/10.1126/science.aaf0643	journal	April 2016
The nuclear pore complex: understanding its function through structural insight Beck, Martin; Hurt, Ed Nature Reviews Molecular Cell Biology, Vol. 18, Issue 2 https://doi.org/10.1038/nrm.2016.147	journal	December 2016
Architecture of the symmetric core of the nuclear pore Lin, D. H.; Stuwe, T.; Schilbach, S. Science, Vol. 352, Issue 6283 https://doi.org/10.1126/science.aaf1015	journal	April 2016
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
A single-domain antibody fragment in complex with RNase A: non-canonical loop structures and nanomolar affinity using two CDR loops Decanniere, Klaas; Desmyter, Aline; Lauwereys, Marc Structure, Vol. 7, Issue 4 https://doi.org/10.1016/S0969-2126(99)80049-5	journal	April 1999
Molecular basis for Nup37 and ELY5/ELYS recruitment to the nuclear pore complex Bilokapic, S.; Schwartz, T. U. Proceedings of the National Academy of Sciences, Vol. 109, Issue 38 https://doi.org/10.1073/pnas.1205151109	journal	September 2012
The Conserved Nup107-160 Complex Is Critical for Nuclear Pore Complex Assembly Walther, Tobias C.; Alves, Annabelle; Pickersgill, Helen Cell, Vol. 113, Issue 2 https://doi.org/10.1016/S0092-8674(03)00235-6	journal	April 2003
Nup153 Recruits the Nup107-160 Complex to the Inner Nuclear Membrane for Interphasic Nuclear Pore Complex Assembly Vollmer, Benjamin; Lorenz, Michael; Moreno-Andrés, Daniel Developmental Cell, Vol. 33, Issue 6 https://doi.org/10.1016/j.devcel.2015.04.027	journal	June 2015
Molecular architecture of the Nup84–Nup145C–Sec13 edge element in the nuclear pore complex lattice Brohawn, Stephen G.; Schwartz, Thomas U. Nature Structural & Molecular Biology, Vol. 16, Issue 11 https://doi.org/10.1038/nsmb.1713	journal	October 2009
Collaboration gets the most out of software Morin, Andrew; Eisenbraun, Ben; Key, Jason eLife, Vol. 2 https://doi.org/10.7554/eLife.01456	journal	September 2013
Removal of a Single Pore Subcomplex Results in Vertebrate Nuclei Devoid of Nuclear Pores Harel, Amnon; Orjalo, Arturo V.; Vincent, Thomas Molecular Cell, Vol. 11, Issue 4 https://doi.org/10.1016/S1097-2765(03)00116-3	journal	April 2003
Modularity within the architecture of the nuclear pore complex Schwartz, Thomas U. Current Opinion in Structural Biology, Vol. 15, Issue 2 https://doi.org/10.1016/j.sbi.2005.03.003	journal	April 2005
Correlative super-resolution fluorescence and electron microscopy of the nuclear pore complex with molecular resolution Löschberger, Anna; Franke, Christian; Krohne, Georg Journal of Cell Science, Vol. 127, Issue 20 https://doi.org/10.1242/jcs.156620	journal	August 2014
Molecular Architecture and Function of the SEA Complex, a Modulator of the TORC1 Pathway Algret, Romain; Fernandez-Martinez, Javier; Shi, Yi Molecular & Cellular Proteomics, Vol. 13, Issue 11 https://doi.org/10.1074/mcp.M114.039388	journal	July 2014
Viral Subversion of the Nuclear Pore Complex Le Sage, Valerie; Mouland, Andrew Viruses, Vol. 5, Issue 8 https://doi.org/10.3390/v5082019	journal	August 2013
Karyopherin-mediated import of integral inner nuclear membrane proteins King, Megan C.; Lusk, C.; Blobel, Günter Nature, Vol. 442, Issue 7106 https://doi.org/10.1038/nature05075	journal	August 2006
Structural and Functional Studies of Nup107/Nup133 Interaction and Its Implications for the Architecture of the Nuclear Pore Complex Boehmer, Thomas; Jeudy, Sandra; Berke, Ian C. Molecular Cell, Vol. 30, Issue 6 https://doi.org/10.1016/j.molcel.2008.04.022	journal	June 2008
The Nuclear Pore Complex Has Entered the Atomic Age Brohawn, Stephen G.; Partridge, James R.; Whittle, James R. R. Structure, Vol. 17, Issue 9 https://doi.org/10.1016/j.str.2009.07.014	journal	September 2009
The Phyre2 web portal for protein modeling, prediction and analysis Kelley, Lawrence A.; Mezulis, Stefans; Yates, Christopher M. Nature Protocols, Vol. 10, Issue 6 https://doi.org/10.1038/nprot.2015.053	journal	May 2015
The Structure of the Scaffold Nucleoporin Nup120 Reveals a New and Unexpected Domain Architecture Leksa, Nina C.; Brohawn, Stephen G.; Schwartz, Thomas U. Structure, Vol. 17, Issue 8 https://doi.org/10.1016/j.str.2009.06.003	journal	August 2009
Nuclear pore complex clustering and nuclear accumulation of poly(A)+ RNA associated with mutation of the Saccharomyces cerevisiae RAT2/NUP120 gene. Heath, C. V.; Copeland, C. S.; Amberg, D. C. Journal of Cell Biology, Vol. 131, Issue 6 https://doi.org/10.1083/jcb.131.6.1677	journal	December 1995
Disruption of the nucleoporin gene NUP133 results in clustering of nuclear pore complexes. Pemberton, L. F.; Rout, M. P.; Blobel, G. Proceedings of the National Academy of Sciences, Vol. 92, Issue 4 https://doi.org/10.1073/pnas.92.4.1187	journal	February 1995
The Nuclear Pore Complex as a Flexible and Dynamic Gate Knockenhauer, Kevin E.; Schwartz, Thomas U. Cell, Vol. 164, Issue 6 https://doi.org/10.1016/j.cell.2016.01.034	journal	March 2016
Structural Evidence for Common Ancestry of the Nuclear Pore Complex and Vesicle Coats Brohawn, S. G.; Leksa, N. C.; Spear, E. D. Science, Vol. 322, Issue 5906 https://doi.org/10.1126/science.1165886	journal	November 2008
Structural and functional analysis of Nup120 suggests ring formation of the Nup84 complex Seo, H. -S.; Ma, Y.; Debler, E. W. Proceedings of the National Academy of Sciences, Vol. 106, Issue 34 https://doi.org/10.1073/pnas.0907453106	journal	August 2009
Nuclear Pore Basket Proteins Are Tethered to the Nuclear Envelope and Can Regulate Membrane Curvature Mészáros, Noémi; Cibulka, Jakub; Mendiburo, Maria Jose Developmental Cell, Vol. 33, Issue 3 https://doi.org/10.1016/j.devcel.2015.02.017	journal	May 2015
The nuclear pore complex: bridging nuclear transport and gene regulation Strambio-De-Castillia, Caterina; Niepel, Mario; Rout, Michael P. Nature Reviews Molecular Cell Biology, Vol. 11, Issue 7 https://doi.org/10.1038/nrm2928	journal	July 2010
Integration, scaling, space-group assignment and post-refinement Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 133-144 https://doi.org/10.1107/S0907444909047374	journal	January 2010
Snapshots of nuclear pore complexes in action captured by cryo-electron tomography Beck, Martin; Lučić, Vladan; Förster, Friedrich Nature, Vol. 449, Issue 7162 https://doi.org/10.1038/nature06170	journal	September 2007
The structure of the COPII transport-vesicle coat assembled on membranes Zanetti, Giulia; Prinz, Simone; Daum, Sebastian eLife, Vol. 2 https://doi.org/10.7554/eLife.00951	journal	September 2013
Structural and functional analysis of Nup133 domains reveals modular building blocks of the nuclear pore complex Berke, Ian C.; Boehmer, Thomas; Blobel, Günter The Journal of Cell Biology, Vol. 167, Issue 4 https://doi.org/10.1083/jcb.200408109	journal	November 2004
Improved low-resolution crystallographic refinement with Phenix and Rosetta DiMaio, Frank; Echols, Nathaniel; Headd, Jeffrey J. Nature Methods, Vol. 10, Issue 11 https://doi.org/10.1038/nmeth.2648	journal	September 2013
Structure of a trimeric nucleoporin complex reveals alternate oligomerization states Nagy, V.; Hsia, K. -C.; Debler, E. W. Proceedings of the National Academy of Sciences, Vol. 106, Issue 42 https://doi.org/10.1073/pnas.0909373106	journal	October 2009
The Yeast Nuclear Pore Complex: Composition, Architecture, and Transport Mechanism Rout, Michael P.; Aitchison, John D.; Suprapto, Adisetyantari The Journal of Cell Biology, Vol. 148, Issue 4 https://doi.org/10.1083/jcb.148.4.635	journal	February 2000
Atomic force microscopy reveals structural variability amongst nuclear pore complexes Stanley, George J.; Fassati, Ariberto; Hoogenboom, Bart W. Life Science Alliance, Vol. 1, Issue 4 https://doi.org/10.26508/lsa.201800142	journal	July 2018
Exploiting Nanobodies’ Singular Traits Ingram, Jessica R.; Schmidt, Florian I.; Ploegh, Hidde L. Annual Review of Immunology, Vol. 36, Issue 1 https://doi.org/10.1146/annurev-immunol-042617-053327	journal	April 2018
A new set of highly efficient, tag-cleaving proteases for purifying recombinant proteins Frey, Steffen; Görlich, Dirk Journal of Chromatography A, Vol. 1337 https://doi.org/10.1016/j.chroma.2014.02.029	journal	April 2014
Architectural Nucleoporins Nup157/170 and Nup133 Are Structurally Related and Descend from a Second Ancestral Element Whittle, James R. R.; Schwartz, Thomas U. Journal of Biological Chemistry, Vol. 284, Issue 41 https://doi.org/10.1074/jbc.M109.023580	journal	August 2009
Optimized E. coli expression strain LOBSTR eliminates common contaminants from His-tag purification : Optimized Andersen, Kasper R.; Leksa, Nina C.; Schwartz, Thomas U. Proteins: Structure, Function, and Bioinformatics, Vol. 81, Issue 11 https://doi.org/10.1002/prot.24364	journal	August 2013
In-cell architecture of the nuclear pore and snapshots of its turnover Allegretti, Matteo; Zimmerli, Christian E.; Rantos, Vasileios Nature, Vol. 586, Issue 7831 https://doi.org/10.1038/s41586-020-2670-5	journal	September 2020
Architecture of a Coat for the Nuclear Pore Membrane Hsia, Kuo-Chiang; Stavropoulos, Pete; Blobel, Günter Cell, Vol. 131, Issue 7 https://doi.org/10.1016/j.cell.2007.11.038	journal	December 2007
Long Unfolded Linkers Facilitate Membrane Protein Import Through the Nuclear Pore Complex Meinema, A. C.; Laba, J. K.; Hapsari, R. A. Science, Vol. 333, Issue 6038 https://doi.org/10.1126/science.1205741	journal	June 2011
Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope Otsuka, Shotaro; Bui, Khanh Huy; Schorb, Martin eLife, Vol. 5 https://doi.org/10.7554/eLife.19071	journal	September 2016
Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex Kampmann, Martin; Blobel, Günter Nature Structural & Molecular Biology, Vol. 16, Issue 7 https://doi.org/10.1038/nsmb.1618	journal	June 2009
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
A Fence-like Coat for the Nuclear Pore Membrane Debler, Erik W.; Ma, Yingli; Seo, Hyuk-Soo Molecular Cell, Vol. 32, Issue 6 https://doi.org/10.1016/j.molcel.2008.12.001	journal	December 2008
Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex : Structure of the Yeast Nup133 C-Terminal Domain Sampathkumar, Parthasarathy; Gheyi, Tarun; Miller, Stacy A. Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue 5 https://doi.org/10.1002/prot.22973	journal	March 2011
Dimerization and direct membrane interaction of Nup53 contribute to nuclear pore complex assembly: Nup53 membrane binding promotes NPC assembly Vollmer, Benjamin; Schooley, Allana; Sachdev, Ruchika The EMBO Journal, Vol. 31, Issue 20 https://doi.org/10.1038/emboj.2012.256	journal	September 2012
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Structure and Assembly of the Nuclear Pore Complex Hampoelz, Bernhard; Andres-Pons, Amparo; Kastritis, Panagiotis Annual Review of Biophysics, Vol. 48, Issue 1 https://doi.org/10.1146/annurev-biophys-052118-115308	journal	May 2019
Nuclear pore complexes exceeding eightfold rotational symmetry Hinshaw, Jenny E.; Milligan, Ronald A. Journal of Structural Biology, Vol. 141, Issue 3 https://doi.org/10.1016/S1047-8477(02)00626-3	journal	March 2003
Integrated Structural Analysis of the Human Nuclear Pore Complex Scaffold Bui, Khanh Huy; von Appen, Alexander; DiGuilio, Amanda L. Cell, Vol. 155, Issue 6 https://doi.org/10.1016/j.cell.2013.10.055	journal	December 2013
Building a nuclear envelope at the end of mitosis: coordinating membrane reorganization, nuclear pore complex assembly, and chromatin de-condensation Schooley, Allana; Vollmer, Benjamin; Antonin, Wolfram Chromosoma, Vol. 121, Issue 6 https://doi.org/10.1007/s00412-012-0388-3	journal	October 2012
Traffic to the inner membrane of the nuclear envelope Laba, Justyna K.; Steen, Anton; Veenhoff, Liesbeth M. Current Opinion in Cell Biology, Vol. 28 https://doi.org/10.1016/j.ceb.2014.01.006	journal	June 2014
Integrative Structure–Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy Molecular & Cellular Proteomics, Vol. 13, Issue 11 https://doi.org/10.1074/mcp.M114.040915	journal	August 2014
Structure and function of WD40 domain proteins Xu, Chao; Min, Jinrong Protein & Cell, Vol. 2, Issue 3 https://doi.org/10.1007/s13238-011-1018-1	journal	March 2011
The Structure of the Nuclear Pore Complex (An Update) Lin, Daniel H.; Hoelz, André Annual Review of Biochemistry, Vol. 88, Issue 1 https://doi.org/10.1146/annurev-biochem-062917-011901	journal	June 2019
Modular self-assembly of a Y-shaped multiprotein complex from seven nucleoporins Lutzmann, Malik; Kunze, Ruth; Buerer, Andrea The EMBO Journal, Vol. 21, Issue 3 https://doi.org/10.1093/emboj/21.3.387	journal	February 2002
Nuclear Pore Complex Is Able to Transport Macromolecules with Diameters of ∼39 nm Panté, Nelly; Kann, Michael Molecular Biology of the Cell, Vol. 13, Issue 2 https://doi.org/10.1091/mbc.01-06-0308	journal	February 2002
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules Ashkenazy, Haim; Abadi, Shiran; Martz, Eric Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw408	journal	May 2016
A Conserved Coatomer-related Complex Containing Sec13 and Seh1 Dynamically Associates With the Vacuole in Saccharomyces cerevisiae Dokudovskaya, Svetlana; Waharte, Francois; Schlessinger, Avner Molecular & Cellular Proteomics, Vol. 10, Issue 6 https://doi.org/10.1074/mcp.M110.006478	journal	March 2011
Structure–function mapping of a heptameric module in the nuclear pore complex Fernandez-Martinez, Javier; Phillips, Jeremy; Sekedat, Matthew D. The Journal of Cell Biology, Vol. 196, Issue 4 https://doi.org/10.1083/jcb.201109008	journal	February 2012
Atomic structure of the Y complex of the nuclear pore Kelley, Kotaro; Knockenhauer, Kevin E.; Kabachinski, Greg Nature Structural & Molecular Biology, Vol. 22, Issue 5 https://doi.org/10.1038/nsmb.2998	journal	March 2015
In situ structural analysis of the human nuclear pore complex von Appen, Alexander; Kosinski, Jan; Sparks, Lenore Nature, Vol. 526, Issue 7571 https://doi.org/10.1038/nature15381	journal	September 2015
Architecture of the nuclear pore complex coat Stuwe, T.; Correia, A. R.; Lin, D. H. Science, Vol. 347, Issue 6226 https://doi.org/10.1126/science.aaa4136	journal	February 2015
Cell Cycle-Dependent Differences in Nuclear Pore Complex Assembly in Metazoa Doucet, Christine M.; Talamas, Jessica A.; Hetzer, Martin W. Cell, Vol. 141, Issue 6 https://doi.org/10.1016/j.cell.2010.04.036	journal	June 2010
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Stoichiometry and compositional plasticity of the yeast nuclear pore complex revealed by quantitative fluorescence microscopy Rajoo, Sasikumar; Vallotton, Pascal; Onischenko, Evgeny Proceedings of the National Academy of Sciences, Vol. 115, Issue 17 https://doi.org/10.1073/pnas.1719398115	journal	April 2018
Establishment of NE asymmetry—targeting of membrane proteins to the inner nuclear membrane Ungricht, Rosemarie; Kutay, Ulrike Current Opinion in Cell Biology, Vol. 34 https://doi.org/10.1016/j.ceb.2015.04.005	journal	June 2015
The Structure Inventory of the Nuclear Pore Complex Schwartz, Thomas U. Journal of Molecular Biology, Vol. 428, Issue 10 https://doi.org/10.1016/j.jmb.2016.03.015	journal	May 2016

Similar Records

Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex

Journal Article · Tue Oct 23 00:00:00 EDT 2012 · Proteins · OSTI ID:1729714

Sampathkumar, Parthasarathy; Gheyi, Tarun; Miller, Stacy A; +18 more

Integrative Structure–Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex

Journal Article · Tue Aug 19 00:00:00 EDT 2014 · Molecular and Cellular Proteomics · OSTI ID:1729714

Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; +13 more

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

Journal Article · Wed Dec 02 00:00:00 EST 2020 · Nature Communications · OSTI ID:1729714

Nordeen, Sarah A.; Andersen, Kasper R.; Knockenhauer, Kevin E.; +3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Title: Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif

Citation Formats

References (75)

Similar Records

Related Subjects