Published October 6, 2016
| Version v1
Dataset
Open
Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform
Creators
- 1. Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY10065, USA
- 2. Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- 3. Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY10065, USA
- 4. Simons Electron Microscopy Center at New York Structural Biology Center, New York, NY 10027, USA
- 5. Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
- 6. Département de Biochimie et médecine moléculaire, University of Montréal, Montréal, QC, Canada
Contributors
Data manager:
- 1. Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
Description
These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the Nup82 complex using DSS/EDC chemical cross-links and electron microscopy (EM) 2D class averages.
First, MODELLER is used to generate initial structures for the individual components in the Nup82 complex. Then, IMP is used to model these components using DSS/EDC crosslinks and the electron microscopy 2D class averages for the entire Nup82 complex.
The modeling protocol will work with a default build of IMP, but for most effective sampling, IMP should be built with MPI so that replica exchange can be used.
For more information about how to reproduce this modeling, see the Sali lab website or the README file.
Files
4_em2d_single_scores_final35r_best.zip
Files
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Additional details
Related works
- Is supplement to
- https://github.com/integrativemodeling/nup82 (URL)
- https://salilab.org/nup82 (URL)
- 27839866 (PMID)