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Elife. 2018 Jun 1;7. pii: e36861. doi: 10.7554/eLife.36861.

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION.

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MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.
Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden.


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.


S. cerevisiae; cryo-electron microscopy; focused refinement; image processing; maximum likelihood; molecular biophysics; single-particle analysis; structural biology

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