These scripts demonstrate the use of IMP in the modeling of the yeast NPC complex using diverse types of data as described in Seung Joong Kim, et al.'s 2018 NPC article published in Nature.

The scripts work with the IMP (version 2.6). A default build of IMP compiled with the IMP::npc module should work, but for most effective sampling, it should be built with MPI so that replica exchange can be used.

List of files and directories:

• input_data_files contains all relevant data

  EMBD_final-yNPC_map_28A.mrc.gz : Cryo-ET density map

  Table1_crosslinks.xlsx : a table of all 3,077 chemical cross-links

  SAXS.zip : SAXS source data (147 SAXS profiles for 18 different Nups) file used for assessment of the NPC structure

• data_npc contains representation (PDB or rmf3 formats), sequence, MODELLER files

  protein_fasta.*.txt : Sequence for each Nups

  *.pdb (or *.rmf3): Representation pdb (or rmf3) files for each Nups

  emd_5556.map : EM 3D density map for Nup192

  XL_optimized_ambiguity.csv : A subset of the chemical cross-links used for the refinement

  XL_Merged_wholeNPC_MLPs : A subset of the chemical cross-links used for the basket components of Mlp1 and Mlp2

• data_npc\Inner_ring_rmfs Representation for the inner ring components

• data_npc\Outer_ring_rmfs Representation for the outer ring components

• data_npc\Pom152_rmfs Representation for the membrane ring (Pom152) component

• data_npc\WholeNPC_rmfs Intermediate files

• data_npc\XL_backup Backup of Chemical cross-links data

• data_npc\em_gmm_model Gaussian Mixture Model (GMM) for each Nups

• data_npc\generating_em_gmm Python scripts to generate Gaussian Mixture Model (GMM) for each Nups

• data_npc\input_contact_frequencies Contact frequency data from the 2007 NPC topological model

• data_npc\input_density_maps Localization probability densities from the 2007 NPC topological model

• data_nic96 contains Nic96 complex-specific representation (PDB or rmf3 formats), sequence (*.txt), cross-links (XLs folder), and EM2D (Nic96complex_classes.hdf) files

• data_nup82 contains Nup82 complex-specific representation (PDB or rmf3 formats), sequence (.txt), cross-links (.csv) files

• data_nup84_2016 contains Nup84 complex-specific representation (PDB or rmf3 formats), sequence (.txt), cross-links (.csv), hhpred (*.pdf or *.webarchive), and EM2D (EM_image.png) files

• pom152 Integrative structure determination of the Pom152 membrane ring - needed to be separate.

• validation contains data not used in modeling

  • nic96_em2d fit of final Nic96 structure against EM class averages

• results contains resulting structures and output files

• template contains modeling scripts

  1_modeling_wholeNPC.py : Initial modeling script

  2_modeling_wholeNPC_FG_anchor_EV.py : Intermediate modeling script

  3_modeling_wholeNPC_refinement.py : Refinement script

  4_modeling_wholeNPC_refinement.py : Final refinement script

  Clustering_RMSD_GPU.py : Clustering script using GPU

  modeling_Nic96complex_initial.py : Initial modeling script for the Nic96 complex components

  modeling_MLPs.py : Refinement script for the basket components

  modeling_pom152.py : Initial modeling script for the membrane-ring (pom152) component

  modeling_pom152_PlaneDihedral.py : Refinement script for the membrane-ring (pom152) component

Compiling IMP with NPC-specific module:

• Clone IMP version 2.6
• Clone the parent repository (npc) into imp/modules/npc/.
• Compile IMP

Running the IMP scripts for the NPC complex:

1. Inner-ring components (Nup157, Nup170, Nup188, Nup192, Nic96, Nup53, Nup59, Ndc1, Pom34, and Pom152 NTD)

• Initial: template/inner_ring/job_IR501-510.sh (running script for template/inner_ring/modeling_inner_ring_initial.py), generates "3IR_502_0.rmf3" (an initial model)
• Refinement : template/inner_ring/job_IR860-869_refinement.sh (running script for template/inner_ring/modeling_inner_ring_refinement.py, which reads "3IR_502_0.rmf3 for the starting coordinate), generates "IR_865_0_final.rmf3" (a refined model).

2. Outer-ring components (Nup82 and Nup84 complexes)

• Initial :

• Refinement :

• cd template

• python XX.py & > XX.out (on a single processor; prepend mpirun -np 6 or similar if you built IMP with MPI support)

or job_test4.sh

Information

Author(s): Seung Joong Kim

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:

• Seung Joong Kim*, Javier Fernandez-Martinez*, Ilona Nudelman*, Yi Shi*, Wenzhu Zhang*, et al., Integrative structure and Functional Anatomy of a Nuclear Pore Complex, Nature 555, 475-482, 2018.