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

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 (VpNup133 55–502) 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 themore » 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.« less

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1352218
Resource Type:
Journal Article
Resource Relation:
Journal Name: Molecular and Cellular Proteomics; Journal Volume: 13; Journal Issue: 11
Country of Publication:
United States
Language:
ENGLISH
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Kim, Seung Joong, Fernandez-Martinez, Javier, Sampathkumar, Parthasarathy, Martel, Anne, Matsui, Tsutomu, Tsuruta, Hiro, Weiss, Thomas M., Shi, Yi, Markina-Inarrairaegui, Ane, Bonanno, Jeffery B., Sauder, J. Michael, Burley, Stephen K., Chait, Brian T., Almo, Steven C., Rout, Michael P., and Sali, Andrej. Integrative Structure–Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex. United States: N. p., 2014. Web. doi: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, Jeffery 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. United States. doi: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, Jeffery B., Sauder, J. Michael, Burley, Stephen K., Chait, Brian T., Almo, Steven C., Rout, Michael P., and Sali, Andrej. Tue . "Integrative Structure–Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex". United States. doi:10.1074/mcp.M114.040915.
@article{osti_1352218,
title = {Integrative Structure–Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex},
author = {Kim, Seung Joong and Fernandez-Martinez, Javier and Sampathkumar, Parthasarathy and Martel, Anne and Matsui, Tsutomu and Tsuruta, Hiro and Weiss, Thomas M. and Shi, Yi and Markina-Inarrairaegui, Ane and Bonanno, Jeffery B. and Sauder, J. Michael and Burley, Stephen K. and Chait, Brian T. and Almo, Steven C. and Rout, Michael P. and Sali, Andrej},
abstractNote = {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.},
doi = {10.1074/mcp.M114.040915},
journal = {Molecular and Cellular Proteomics},
number = 11,
volume = 13,
place = {United States},
year = {Tue Aug 19 00:00:00 EDT 2014},
month = {Tue Aug 19 00:00:00 EDT 2014}
}