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

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 inde...

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Vydáno v:eLife Ročník 7
Hlavní autoři: Nakane, Takanori, Kimanius, Dari, Lindahl, Erik, Scheres, Sjors HW
Médium: Journal Article
Jazyk:angličtina
Vydáno: England eLife Sciences Publications, Ltd 01.06.2018
eLife Sciences Publications Ltd
Témata:
Biochemistry towards Bioinformatics
biokemi med inriktning mot bioinformatik
cryo-electron microscopy
Cryoelectron Microscopy
focused refinement
image processing
Image Processing, Computer-Assisted
maximum likelihood
Models, Molecular
Motion
Plasmodium falciparum - metabolism
Ribosomes - metabolism
Saccharomyces cerevisiae
single-particle analysis
Software
Spliceosomes - metabolism
Structural Biology and Molecular Biophysics
Tools and Resources
image processing
focused refinement
maximum likelihood
structural biology
molecular biophysics
S. cerevisiae
cryo-electron microscopy
single-particle analysis
ISSN:2050-084X, 2050-084X
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Shrnutí: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.
Bibliografie:ObjectType-Article-1
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content type line 23
ISSN:2050-084X
2050-084X
DOI:10.7554/eLife.36861