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Pol II (G) complex

Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1 PubMed logo PDB-Dev

warningThese files work only with a nightly build of IMP on or after 2018-12-08, not the stable release. The files are also available at GitHub.
Additional software needed to use these files: IMP numpy 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

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

module load imp python/numpy
Tags chemical crosslinks EM PMI

DOI

Localizing gdown1 on POL II using integrative structure modeling

These scripts demonstrate the use of IMP and PMI in the modeling of the Pol II(G) complex using DSS chemical cross-links.

Input data (directory data):

40 DSS cross-links involving gdown1 were identified via mass spectrometry. 14 of these cross-links were intramolecular and 26 were intermolecular with Pol II. The Pol II structure used was obtained from the PDB (code 5FLM); it was determined primarily based on a cryo-EM density map at 3.4 Å resolution (EMDB code: 3218) Bernesky, 2016 Nature.

Representation of gdown1 relied on (i) secondary structure and disordered regions predicted by PSIPRED based on the gdown1 sequence (Buchan et al., 2013; Jones, 1999).

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)

Python scripts for generating figures from the paper.

Information

Author(s): Sai J. Ganesan

Date: September 6th, 2018

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: Miki Jishage, Xiaodi Yu, Yi Shi, Sai J. Ganesan, Andrej Sali, Brian T. Chait, Francisco Asturias, and Robert G. Roeder Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1 Nat Struct Mol Biol. (2018) 25(9):859-867. doi: https://doi.org/10.1038/s41594-018-0118-5