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Integrative structure determination of the Pks13 dimer

Summary

A structural model of the Pks13 dimer was computed by integrative modeling based on the 57 DSSO chemical cross-links and structural models of the components of the Pks13 dimer. These components include the atomic structural model based on the cryo-EM maps (EMD-26574), de novo AlphaFold2 predictions of domains unresolved in the cryo-EM structure and flexible linker regions. A model of the Pks13 dimer was computed by satisfying this input information to the best possible degree using IMP. The resulting ensemble of acceptable models satisfies 91% of the cross-links.

List of files and directories:

  • data All data used for integrative modeling, including the cross-links, the partial Pks13 structure obtained using cryo-EM, and the AlphaFold model.
  • scripts PMI modeling script (mod_symmetry.py) to model the symmetry full-lenght Pks13 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: Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Sun Kyung Kim, Miles Sasha Dickinson,, Janet Finer-Moore, Ziqiang Guan, Robyn M. Kaake, Ignacia Echeverria, Jen Chen, Ernst H. Pulido, Andrej Sali, Nevan J. Krogan, Oren S. Rosenberg, Robert M. Stroud, Nature Structural & Molecular Biology. 2022