Title: Modeling of the Nup84 subcomplex of the Nuclear Pore Complex

Type Dataset Shi, Yi, Fernandez-Martinez, Javier, Tjioe, Elina, Pellarin, Riccardo, Kim, Seung Joong, Williams, Rosemary, Schneidman-Duhovny, Dina, Rout, Michael, Sali, Andrej, Chait, Brian (2014): Modeling of the Nup84 subcomplex of the Nuclear Pore Complex. Zenodo. Dataset. https://zenodo.org/record/1218053

Authors: Shi, Yi (Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065) ; Fernandez-Martinez, Javier (Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065) ; Tjioe, Elina (Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158) ; Pellarin, Riccardo (Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158) ; Kim, Seung Joong (Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158) ; Williams, Rosemary (Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065) ; Schneidman-Duhovny, Dina (Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158) ; Rout, Michael (Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065) ; Sali, Andrej (Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, California 94158) ; Chait, Brian (Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065) ; Webb, Benjamin (University of California, San Francisco, United States.) ;

Links

• Item record in Zenodo
• Digital object URL

Summary

These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the Nup84 complex using 286 DSS/EDC chemical cross-links and an electron microscopy (EM) 2D class average.

First, MODELLER is used to generate initial structures for the individual components in the Nup84 complex. Then, IMP is used to model these components using DSS/EDC crosslinks and the electron microscopy 2D class average for the entire Nup84 complex.

For more information about how to reproduce this modeling, see the Sali lab website or the README file.

More information

• DOI: 10.5281/zenodo.1218053

Subjects

• Integrative Modeling Platform (IMP), Chemical crosslinks, Electron microscopy class average, MODELLER, PMI

Dates

• Publication date: 2014
• Issued: August 26, 2014

Rights

• https://opensource.org/licenses/LGPL-2.1 GNU Lesser General Public License v2.1 only
• info:eu-repo/semantics/openAccess Open Access

Format

electronic resource

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