Dataset Open Access

Modeling of the Nup133 subunit of the yeast 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, Jeffery B.; Sauder, J. Michael; Burley, Stephen K.; Chait, Brian T.; Almo, Steven C.; Rout, Michael P.; Sali, Andrej

Data manager(s)
Webb, Benjamin

These scripts demonstrate the use of IMPMODELLERFoXS, 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 (384.0 MB)
Name Size
Crosslinks.zip
md5:e6fd3f208c8d7756267c04177f8abe03
770.5 kB Download
ISAC.zip
md5:23f8c11e4e70034debea2933a0d5566d
3.8 MB Download
MODELLER.zip
md5:65150b4f0742f6d421a761ff991904a0
178.2 kB Download
nup133-master.zip
md5:1aee2e74809a35984840904f529f221a
373.2 MB Download
SAXS.zip
md5:8cb99e5aed11c8101464b3d45b50d342
6.1 MB Download
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