Dataset Open Access

Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform

Fernandez-Martinez, Javier; Kim, Seung Joong; Shi, Yi; Upla, Paula; Pellarin, Riccardo; Gagnon, Michael; Chemmama, Ilan E.; Wang, Junjie; Nudelman, Ilona; Zhang, Wenzhu; Williams, Rosemary; Rice, William J.; Stokes, David L.; Zenklusen, Daniel; Chait, Brian T.; Sali, Andrej; Rout, Michael P.

Data manager(s)
Webb, Benjamin

These scripts demonstrate the use of IMPMODELLER, 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 (4.0 GB)
Name Size
1_initial_Random.tar.xz
md5:9971534cb1fadfd59e70153f32a312af
3.2 GB Download
2_allEM2D.tar.xz
md5:38082d2db36701fffe65633c8cc913e1
522.6 MB Download
4_em2d_single_scores_final35r_best.zip
md5:908470e507ae163f957bd23ad93145d6
983.2 kB Download
4ycz_3ewe.zip
md5:72ebb4ba74f774f43cd2f2fec22f384c
2.2 MB Download
5_GFP.zip
md5:2a470aab5bdc5c943a5605614375a01f
11.8 MB Download
6_Nup82Nup84.zip
md5:4b456d10253997c732d754ebc8f44a23
69.1 MB Download
back_up.zip
md5:41116e61c16a1e201472f32234324594
4.5 MB Download
cluster.0.zip
md5:c972e7ab1e2fca261e43f6ddab779f47
521.9 kB Download
cluster.1.zip
md5:4edb3227e7be58f18299f2f1dd334854
505.5 kB Download
cluster0.dcd
md5:7187c47150ac9d74121c378179cc4981
14.5 MB Download
cluster1.dcd
md5:ef3aec17ebe30b19a3f868d4bf183e22
3.7 MB Download
data.zip
md5:0e74f90f5e6a01bba77dfaeb9257d31a
2.1 MB Download
em2d.zip
md5:54cd65c19d6551466998c04bd64bf484
1.1 MB Download
em2d_without_bg.zip
md5:908dd726c8c53dc9a0b1b0199715f8af
310.7 kB Download
MODELLER.zip
md5:fce91e7045ddfbda1f38a95b2d885e4c
8.2 MB Download
nup82-master.zip
md5:960376be823f15157a0bdfff78278fc5
28.8 MB Download
outputs.zip
md5:f98509bedc3972c8cbdd296367332b2b
71.3 MB Download
SAXS.zip
md5:82b7c950226beeae9fc3a195cc6fa10a
5.5 MB Download
template.zip
md5:a35a2194bc24207b6d422838591de84a
122.8 kB Download
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