Published September 2, 2014
| Version v2
Dataset
Open
Modeling of the Nup133 subunit of the yeast Nuclear Pore Complex
Authors/Creators
- Kim, Seung Joong1
- Fernandez-Martinez, Javier2
- Sampathkumar, Parthasarathy3
- Martel, Anne4
- Matsui, Tsutomu4
- Tsuruta, Hiro4
- Weiss, Thomas M.4
- Shi, Yi5
- Markina-Inarrairaegui, Ane6
- Bonanno, Jeffery B.3
- Sauder, J. Michael7
- Burley, Stephen K.8
- Chait, Brian T.5
- Almo, Steven C.3
- Rout, Michael P.2
- Sali, Andrej1
- 1. 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
- 2. Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065
- 3. Department of Biochemistry, Ullmann Building, Room 409, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
- 4. Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, MS 69, Menlo Park, California 94025
- 5. Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065
- 6. Laboratorio de Genetica Molecular de Aspergillus, Departamento de Biología Celular y Molecular, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
- 7. Discovery Chemistry Research and Technologies (DCR&T), Eli Lilly and Company, Lilly Biotechnology Center, 10300 Campus Point Drive, Suite 200, San Diego, California 92121
- 8. Center for Integrative Proteomics Research, Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, 174 Frelinghuysen Road, Piscataway, New Jersey 08854
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, FoXS, and AllosMod, and Minimal Ensemble Search in the modeling of the Nup133 protein in the S. cerevisiae Nuclear Pore Complex (NPC). First, MODELLER is used to generate an initial comparative model of Nup133 guided by FoXS fits to SAXS data. Then, the model was subjected to conformational sampling with AllosMod, and finally Minimal Ensemble Search was used to identify four models that together reproduced both the SAXS data and a set of electron microscopy class averages. The final model was also validated against a set of chemical cross-links, that were not used in the modeling.
For more information about how to reproduce this modeling, see the Sali lab website or the README file.
Files
Crosslinks.zip
Files
(384.0 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/integrativemodeling/nup133 (URL)
- https://salilab.org/nup133 (URL)
- 25139911 (PMID)