Integrative structural modelling of macromolecular complexes using Assembline

Abstract

Integrative modelling enables structure determination of macromolecular complexes by combining data from multiple experimental sources such as X-ray crystallography, electron microscopy (EM), or crosslinking mass spectrometry (XL-MS). It is particularly useful for complexes not amenable to high-resolution EM-complexes that are flexible, heterogenous, or imaged in cells with cryo-electron tomography. We have recently developed an integrative modelling protocol that allowed us to model multi-megadalton complexes as large as the nuclear pore complex. Here, we describe the Assembline software package, which combines multiple programs and libraries with our own algorithms in a streamlined modelling pipeline. Assembline builds ensembles of models satisfying data from atomic structures or homology models, EM maps and other experimental data, and provides tools for their analysis. Comparing to other methods, Assembline enables efficient sampling of conformational space through a multi-step procedure, provides new modeling restraints, and includes a unique configuration system for setting up the modelling project. Our protocol achieves exhaustive sampling in less than 100 - 1,000 CPU-hours even for complexes in the megadalton range. For larger complexes, resources available in institutional or public computer clusters are needed and sufficient to run the protocol. We also provide step-by-step instructions for preparing the input, running the core modelling steps, and assessing modelling performance at any stage.

Structure of the mycobacterial ESX-5 type VII secretion system pore complex

“…The models of the hexameric assembly of the periplasmic domains of EccB 5 (amino acids 74 to 490) and cytoplasmic ATPase domains of EccC 5 (amino acids 431 to 1390) were built using an integrative modeling protocol similar to what was previously used by us ( 43 – 45 ). The modeling procedure described in more detail below is implemented as a custom software based on Integrative Modeling Platform ( 46 ) version 2.13 and Python Modeling Interface ( 47 ) further described in ( 48 ). All additional code and input files necessary to reproduce the steps will be released on Zenodo repository upon publication.…”

Nuclear pores dilate and constrict in cellulo

“…Structural models of the SpNPCs were built using the integrative procedure (fig. S5) implemented in our Assembline software (92). Assembline implements a custom modeling pipeline based on Integrative Modeling Platform (IMP) (93) version 2.14 and Python Modeling Interface (PMI) (94).…”

Artificial intelligence reveals nuclear pore complexity

“…We then added the remaining newly modeled subunits by systematic fitting to the EM map and refinement using the Assembline program (37). In addition to fitting the models, we have added several disordered linkers that connect spatially separated domains and SLiMs within the NPC.…”