Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex

Seung Joong Kim, Javier Fernandez-Martinez, Parthasarathy Sampathkumar, Anne Martel, Tsutomu Matsui, Hiro Tsuruta, Thomas M. Weiss, Yi Shi, Ane Markina-Inarrairaegui, Jeffrey B. Bonanno, J. Michael Sauder, Stephen K. Burley, Brian T. Chait, Steven C. Almo, Michael P. Rout, Andrej Sali

Research output: Contribution to journalArticle

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Abstract

The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup13355-502) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one construct of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup1332-1157. Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes.

Original languageEnglish (US)
Pages (from-to)2911-2926
Number of pages16
JournalMolecular and Cellular Proteomics
Volume13
Issue number11
DOIs
StatePublished - Nov 1 2014

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Nuclear Pore Complex Proteins
Nuclear Pore
Membranes
Nuclear Envelope
Lipids
Scaffolds
Yeast
Saccharomyces cerevisiae
Sensors
Coatings
Structural Models
Eukaryota
X ray scattering
Macromolecules
Electron microscopy
Mass spectrometry
Mass Spectrometry
Electron Microscopy
Coloring Agents
Crystal structure

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Analytical Chemistry

Cite this

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; Martel, Anne; Matsui, Tsutomu; Tsuruta, Hiro; Weiss, Thomas M.; Shi, Yi; Markina-Inarrairaegui, Ane; Bonanno, Jeffrey B.; Sauder, J. Michael; Burley, Stephen K.; Chait, Brian T.; Almo, Steven C.; Rout, Michael P.; Sali, Andrej.

In: Molecular and Cellular Proteomics, Vol. 13, No. 11, 01.11.2014, p. 2911-2926.

Research output: Contribution to journalArticle

Kim, SJ, Fernandez-Martinez, J, Sampathkumar, P, Martel, A, Matsui, T, Tsuruta, H, Weiss, TM, Shi, Y, Markina-Inarrairaegui, A, Bonanno, JB, Sauder, JM, Burley, SK, Chait, BT, Almo, SC, Rout, MP & Sali, A 2014, 'Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex', Molecular and Cellular Proteomics, vol. 13, no. 11, pp. 2911-2926. https://doi.org/10.1074/mcp.M114.040915
Kim, Seung Joong ; Fernandez-Martinez, Javier ; Sampathkumar, Parthasarathy ; Martel, Anne ; Matsui, Tsutomu ; Tsuruta, Hiro ; Weiss, Thomas M. ; Shi, Yi ; Markina-Inarrairaegui, Ane ; Bonanno, Jeffrey B. ; Sauder, J. Michael ; Burley, Stephen K. ; Chait, Brian T. ; Almo, Steven C. ; Rout, Michael P. ; Sali, Andrej. / Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex. In: Molecular and Cellular Proteomics. 2014 ; Vol. 13, No. 11. pp. 2911-2926.
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AU - Fernandez-Martinez, Javier

AU - Sampathkumar, Parthasarathy

AU - Martel, Anne

AU - Matsui, Tsutomu

AU - Tsuruta, Hiro

AU - Weiss, Thomas M.

AU - Shi, Yi

AU - Markina-Inarrairaegui, Ane

AU - Bonanno, Jeffrey B.

AU - Sauder, J. Michael

AU - Burley, Stephen K.

AU - Chait, Brian T.

AU - Almo, Steven C.

AU - Rout, Michael P.

AU - Sali, Andrej

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N2 - The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup13355-502) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one construct of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup1332-1157. Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes.

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