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Model of Ecm29-proteasome complex

Regulation of 26S proteasome via interaction with Ecm29 PubMed logo PDB-Dev

tickVerified to work with the latest stable IMP release (2.9.0). The files are also available at GitHub.
Additional software needed to use these files: IMP numpy MODELLER 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 modeller

UCSF logo To set up the environment on the UCSF QB3 cluster to run this system, run:

module load imp python/numpy modeller
Tags chemical crosslinks PMI X-ray

DOI

Localizing ecm29 on the proteasome using integrative structure modeling

These scripts demonstrate the use of IMP, MODELLER, and PMI in the modeling of the proteasome/ecm29 complex using DSSO chemical cross-links.

Comparative modeling of ecm29 (2 domains)

Representation of ecm29 relied on (i) comparative models of 2 ecm29 domains built with MODELLER 9.17 (Sali and Blundell, 1993) based on the known related structures detected by HHPred (Soding, 2005; Soding et al. 2005) and (ii) secondary structure and disordered regions predicted by PSIPRED based on the ecm29 sequence (Buchan et al., 2013; Jones, 1999); see file ecm29.hhp in the comparative_modeling directory.

The sequences of the two templates (1U6G and 3W3W) and ecm29 can be found in template.ali. The two templates have PDB code 1U6G and 3W3W respectively, with alignment to ecm29 in aligs.pir. To obtain the comparative models, run model_ecm29_352.py and model_ecm29_686.py.

Input data (directory data):

63 DSSO cross-links involving ecm29 were identified via mass spectrometry; 56 of these cross-links were intramolecular and seven were intermolecular with the 19S proteasome, informing respectively the ecm29 conformation and the localization of ecm29 relative to the proteasome.

The 26S proteasome structure used was obtained from the PDB (code 5GJR); it was determined primarily based on a cryo-EM density map at 3.8Å resolution (EMDB code: 9508) {Huang, 2016 NSMB}.

Running the simulations (directory production_scripts):

Analyzing the simulations (directory analysis_scripts):

Various scripts to analysis the simulations. we give more details scripts that allows us to test for sampling convergence.

Plotting the results (directory plotting_scripts)

GNUPlot scripts for generating figures from the paper.

Information

Author(s): Ilan E. Chemmama

Date: November 3rd, 2016; Updated August 16, 2017.

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

Parallelizeable: Yes

Publications: Xiaorong Wang, Ilan E Chemmama, Clinton Yu, Alexander Huszagh, Yue Xu, Rosa Viner, Sarah Ashley Block, Peter Cimermancic, Scott D Rychnovsky, Yihong Ye, Andrej Sali, and Lan Huang The Proteasome-Interacting Ecm29 Protein Disassembles the 26S Proteasome in Response to Oxidative Stress J. Biol. Chem. jbc.M117.803619. doi:10.1074/jbc.M117.803619