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Smc5/6-Nse2/5/6 complex

Integrative modeling of the Smc5/6-Nse2/5/6 complex using comparative modeling and chemical crosslinks. PubMed logo PDB-Dev

tickVerified to work with the latest stable IMP release (2.15.0). The files are also available at GitHub.
Additional software needed to use these files: IMP numpy pandas matplotlib MODELLER biopython install instructions

Anaconda logo To install the software needed to reproduce this system with the Anaconda Python command line tool (conda), run the following commands:

conda config --add channels salilab
conda install imp numpy pandas matplotlib modeller biopython

UCSF logo To set up the environment on the UCSF Wynton cluster to run this system, run:

module load Sali
module load imp python3/numpy python3/pandas python3/matplotlib modeller python3/biopython
Tags chemical crosslinks coiled-coils cryo-EM ISAMBARD PMI X-ray

DOI

Integrative structure of the Smc5/6-Nse2/5/6 complex

This repository contains Python scripts and associated input data and output results for constructing the integrative model of the ATP-bound five-subunit yeast Smc5/6-Nse2/5/6 complex, using IMP, (develop-255ae6c), PMI and MODELLER.

The input data used for this work is:

First, comparative models of the different parts of Smc5/6 as mentioned above, are constructed using both MODELLER and the SWISS-MODEL webserver. Next, parametric models of the coiled-coil regions of Smc5/6 arms are designed using the protein design software package ISAMBARD. Finally, models of these different components are put together and the crosslink information is used to create spatial restraints and derive the overall model of the five subunit complex using IMP. 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.

List of files and directories:

Worfklow

Comparative modeling

First, non-comparative models are generated following the steps outlined in the jupyter notebook non_cc_comparative_modeling/modeling.ipynb. The model of Smc5/6 head regions is generated by running the MODELLER script non_cc_comparative_modeling/smc56_head_MODELLER/modeling.py as:

cd non_cc_comparative_modeling/smc56_head_MODELLER
python modeling.py

This will produce all output files and a log file (log.txt) in this directory. To keep things clean, all of this output has been stored in a separate subfolder non_cc_comparative_modeling/smc56_head_MODELLER/output. The final models produced from this step are all stored in non_cc_comparative_modeling/best_models and should be copied over to data/pdb to be used later in integrative modeling.


Coiled-coil modeling

Next, coiled-coil models are designed by searching in a parameter space spanned by geometrical descriptors of coiled-coil structures using the ISAMBARD software package. The motivation and all necessary steps are outlined in the notebook cc_parameteric_modeling/modeling.ipynb and demonstrated in detail for a specific example of the Smc5 coiled coil region adjacent to the head region. The protocol is similar for other coiled coil segments. The final models produced from this step are all stored in cc_parametric_modeling/best_models and should be copied over to data/pdb to be used later in integrative modeling.


Integrative modeling

At this stage, PDB files corresponding to different rigid bodies in the complex must be ready and kept in data/pdb. The rigid body definitions can be found in the PMI topology file data/topology.txt. All python scripts in this folder can be run with a -h flag, i.e. python <script name> -h to see its usage, inputs, expected outputs, etc.

Structural calculations on the integrative models

The integrative model is represented not only by the centroid, but the ensemble of all good scoring models in the most populated cluster. To extract structural metrics like Smc5/6 arm length, etc, the calculation should be repeated for all models in the top-cluster so as to produce a mean and an error-bar for that metric. All of these results are kept in integrative_modeling/structural_calculations. To calculate crosslink satisfaction (and store the results in a folder called structural_calculations/xl_satisfaction):

cd integrative_modeling/structural_calculations
python ../get_XL_satisfaction.py -r ../structural_clustering/good_scoring_models.rmf3 -c 0 -m ../structural_clustering/sp_50/cluster.0.all.txt -xl ../../data/xl/xl_all.csv -o ./xl_satisfaction/

To calculate Smc5/6 arm geometry related metrics (and store it in a file called structural_calculations/Smc56_arm_geometry.txt):

cd integrative_modeling/structural_calculations
python ../get_Smc56_arm_geometry.py -r ../structural_clustering/good_scoring_models.rmf3 -c 0 -m ../structural_clustering/sp_50/cluster.0.all.txt -o .

Information

Author(s): Tanmoy Sanyal

Date: April 13, 2021

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: build info build info

Testable: Yes.

Parallelizable: Yes

Publications: You Yu, Shibai Li, Zheng Ser, Tanmoy Sanyal, Koyi Choi, Bingbing Wan, Huihui Kuang, Andrej Sali, Alex Kentsis, Dinshaw J. Patel and Xiaolan Zhao, Integrative analysis reveals unique structure and function features of the Smc5/6 complex, bioRxiv (2020)