Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION
- MRC Laboratory of Molecular Biology, United Kingdom
- Stockholm University, Sweden
Abstract
Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. We describe a new tool, called multi-body refinement, which models flexible complexes as a user-defined number of rigid bodies that move independently from each other. Using separate focused refinements with iteratively improved partial signal subtraction, the new tool generates improved reconstructions for each of the defined bodies in a fully automated manner. Moreover, using principal component analysis on the relative orientations of the bodies over all particle images in the data set, we generate movies that describe the most important motions in the data. Our results on two test cases, a cytoplasmic ribosome from Plasmodium falciparum, and the spliceosomal B-complex from yeast, illustrate how multi-body refinement can be useful to gain unique insights into the structure and dynamics of large and flexible macromolecular complexes.
Data availability
The spliceosome and ribosome datasets have been uploaded to the EMPIAR database. Their entry numebrs are 10180 and 10028 respectively
Article and author information
Author details
Funding
Medical Research Council (MC UP A025 1013)
- Sjors HW Scheres
Svenska Forskningsrådet Formas (2017-04641)
- Erik Lindahl
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2018, Nakane et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION
eLife 7:e36861.
https://doi.org/10.7554/eLife.36861
