Integrative structure determination of the Pom34-152 transmembrane

attachment site

Summary

A structural model of the Pom34-152 transmembrane attachment site dimer was computed by integrative modeling based on the cryo-EM density maps (EMD-41117) and the AlphaFold2 structure predcition of the monomers. A model of the dimer Pom34-152 transmembrane domains (TMDs) was computed by satisfying this input information to the best possible degree using IMP.

List of files and directories:

• data All data used for integrative modeling, including the cross-links, EM density map, and the AlphaFold2 models.
• scripts PMI modeling script (mod_TMDs.py) to model the symmetric Pom34-152 dimer.
• analysis Scripts to analyze the simulations
• results All the relevant results from integrative modeling, including the distance statistics for the cross-links and clustering of the results.
• SI_table Scripts to generate a table summarizing the integrative modeling protocols.
• utils Template and code to generate the Supporting information table summarizing the integrative modeling protocol.

Information

Author (s): Ignacia Echeverria

License: CC BY-SA 4.0 This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License.

Publications: Implications of a multiscale structure of the yeast Nuclear Pore Complex. Akey CA, Echeverria I, Ouch C, Nudelman I, Shi Y, Wang J, Weiss TM, Shi Y, Chait BT, Sali A,Fernandez-Martinez J, Rout MP. Molecular Cell. 2023