Integrative model of the γTuSC-Spc110 complex

This repository pertains to the integrative model of the γTuSC-Spc110 complex based on data from cryo-EM, chemical crosslinking, and X-ray crystallography.

The repository contains input data, scripts for modeling and results including bead models and localization probability density maps. It uses IMP (Integrative Modeling Platform).

Folder structure:

1. inputs : contains all the input data used for modeling such as PDB files and crosslink files.
2. scripts : scripts to prep input files, perform sampling, and analysis are provided.
3. results : contains the models and localization densities of the top cluster.
4. test : scripts for testing the sampling

Protocol:

Simulations

There are three independent simulations:

1. Modeling of one copy of γTuSC bound to Spc110 dimer : gtusc_spc110dimer or dimer
2. Modeling of one copy of γTuSC bound to Spc110 monomer : gtusc_spc110monomer or monomer
3. Modeling of two copies of laterally associated γTuSC bound to one Spc110 dimer each : lateral_gtusc_spc110tetramer or tetramer

Sampling

To run the sampling, run modeling scripts like this

mpirun -np 6 $IMP python scripts/sample/sample_SCRIPTNAME.py prod

where $IMP is the setup script corresponding to the IMP installation directory (omit for binary installation)
and SCRIPTNAME can be, for example, gtusc_110dimer_1-220GCN4_nointra110xlinks for the dimer simulations.

50 production runs were performed in the above manner for each of the simulations.

Analysis

Good scoring models were selected using imp-sampcon as shown in scripts/analysis/get_gsms.sh

Sampling exhaustiveness tests were performed using imp-sampcon as shown in scripts/analysis/sampcon.sh

Crosslink violations were analyzed using scripts/analysis/get_xlink_violations_gtuscSpc110.py

Results

For each of the simulations, the following files are in the results directory

• cluster_center_model.rmf3 : representative bead model of the major cluster
• densities_session.py : to view the localization densities (.mrc files)
• crosslink_violations_*.txt : list of violated crosslinks

Information

Author(s): Shruthi Viswanath

Date: Dec 2nd, 2020

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

Last known good IMP version:

Testable: Yes.

Parallelizeable: Yes

Publications:

• Brilot, Axel F., Andrew Lyon, Alex Zelter, Shruthi Viswanath, Alison Maxwell, Michael J. MacCoss, Eric G. Muller, Andrej Sali, Trisha N. Davis, and David A. Agard. "CM1-driven assembly and activation of Yeast γ-Tubulin Small Complex underlies microtubule nucleation." eLife, 10:e65168, 2021.