Pom152

This repository contains the modeling files and the analysis related to the article "Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex" by Upla et al. in Structure 2017. The scripts work with IMP (version 2.6 or later).

List of files and directories:

• data contains all relevant data

  *.pdb : Representation PDB for individual domains

  *.csv : Cross-links data for further validation

  FASTA_*.txt : Sequence files

  data/Cadherin : sequence and structure alignments between Cadherin and Pom152

  data/em2d_T1_truncation_1-1135 : EM 2D class averages of the Pom152 1-1135 (truncated)

  data/em2d_T2_truncation_1-936 : EM 2D class averages of the Pom152 1-936 (truncated)

  data/em2d_WT : EM 2D class averages of the full length Pom152

  data/em3d_density : EM 3D density map of the full length Pom152

  data/HHPred : Template search results using HHPred

  data/MODELLER_all : Comparative models generated using MODELLER

  data/Pom152_comparative_models_by_SAXS : Best-scoring comparative models filtered by the corresponding SAXS data

• template contains modeling scripts

  modeling_pdb375_482.py : modeling script

• results contains resulting structures and output files

  results/EM2D_selected : Validation of the Pom152 structure using selected EM 2D class averages (using multiple resolutions ranging 35 - 80 Å)

  results/Pom152_em3d_Final : Best-scoring Pom152 structures (clusters 0 and 1) and localization probability density maps

  results/Pom152_em3d_with_Rotational_Restraint : Refined Pom152 structure using a dihedral restraint (holding a 90 degree rotation between neighboring Ig-fold domains)

• prefilter Selection of 500 good-scoring models ranked by the combined total score. Also score log files (*.log) are included

• analysis contains Clustering scripts and results

Running the MODELLER scripts:

First, comparative models were built for each domain of Pom152:

• cd data/MODELLER_all
• (cd 375-482 && python all_sjkim_final.py > all_sjkim_final.log) : Residues 375-482
• (cd 516-611 && python all_sjkim_final.py > all_sjkim_final.log) : Residues 516-611
• (cd MODELLER_27005 && python all_sjkim_final.py > all_sjkim_final.log) : Residues 603-828
• (cd MODELLER_26996 && python all_sjkim_final.py > all_sjkim_final.log) : Residues 718-1156
• (cd 1146-1237 && python all_sjkim_final.py > all_sjkim_final.log) : Residues 1146-1237
• (cd 1238-1337 && python all_sjkim_final.py > all_sjkim_final.log) : Residues 1238-1337

Running the IMP/PMI scripts:

Next, integrative modeling was carried out, taking the comparative models and experimental data as input, followed by clustering and analysis:

• (cd template && python modeling_pdb375_482.py)
• (cd analysis && python clustering.py && python precision_rmsf.py -dir kmeans_1000_2)

Information

Author(s): Seung Joong Kim

Date: March 2017

License: CC-BY-SA-4.0. This work is freely available under the terms of the Creative Commons Attribution-ShareAlike 4.0 International License.

Last known good IMP version:

Publications:

• Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, Williams R, Bonanno JB, Rice WJ, Stokes DL, Cowburn D, Almo SC, Sali A, Rout MP, Fernandez-Martinez J. Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex, Structure, 2017, 10.1016/j.str.2017.01.006.