Tutorial: integrative modelling of S. cerevisiae nuclear pore complex (ScNPC) using Assembline

Assembline is a software for integrative structural modelling of macromolecular assemblies - an assembly line of macromolecular assemblies!

This tutorial demonstrates the usage of Assembline on an example of S. cerevisiae nuclear pore complex (ScNPC) from wild-type (wt) and Nup116 (NPC member protein) knock-out (k.o.) cells. By following the detailed data preparation and modelling steps for Assembline the users will be able to reproduce our previously published integrative models (Allegretti et al. (2020)) of: Cytoplasmic Ring Y-complex (CR Y-complex), Inner Ring asymmetric unit (IR asymmetric unit), Nuclear Ring Y-complex (NR Y-complex), Nup116 k.o. ScNPC (at 25C), Nup116 k.o. ScNPC (at 37C).

• All the necessary input data and modelling templates are provided (as well as some precalculated output) and should be downloaded from our ScNPC_tutorial git repository. In this repository you will find the following directories which include all relevant files per modelling target (subcomplexes and k.o. ScNPC models)

  CR_Y_complex
  IR_asymmetric_unit_refinement
  NR_Y_complex
  Nup116delta25C
  Nup116delta37C
  

Note

In case you want to directly jump to modelling ScNPCs hence skipping the theory, set ups and general usage instructions then you can continue from the CR Y-complex modelling.

Use the Next button at the bottom right or menu on the left to navigate through the tutorial.

• About the S. cerevisiae nuclear pore complex (ScNPC)

Data preparation

• Data preparation

Calculation of fit libraries

• About fit libraries
• Set up
• Run
• Analyze fits
  • Check if run correctly

Global optimization

• Setting up the JSON project file
  • Create Xlink Analyzer project
  • Add modelling information to the project file
• Setting up the parameter file
• Run
• Analyze
  • Extract scores
  • Create a CIF file of the top N models
  • Assess sampling exhaustiveness

Refinement

• Setting up the JSON project file
• Setting up the parameter file
• Run
• Analyze

CR Y-complex modelling

• CR Y-complex modelling

IR asymmetric unit modelling

• IR asymmetric unit modelling

NR Y-complex modelling

• NR Y-complex modelling

Modelling of Nup116 k.o. ScNPC (at 25C)

• Nup116 k.o. ScNPC (at 25C) modelling

Modelling of Nup116 k.o. ScNPC (at 37C)

• Nup116 k.o. ScNPC (at 37C) modelling