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Scheres, Sjors H. W.ORCID iD iconorcid.org/0000-0002-0462-6540
Publications (2 of 2) Show all publications
Nakane, T., Kimanius, D., Lindahl, E. & Scheres, S. H. W. (2018). Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION. eLIFE, 7, Article ID e36861.
Open this publication in new window or tab >>Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION
2018 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 7, article id e36861Article in journal (Refereed) Published
Abstract [en]

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.

National Category
Biological Sciences
Research subject
Biochemistry towards Bioinformatics
Identifiers
urn:nbn:se:su:diva-158144 (URN)10.7554/eLife.36861 (DOI)000435436100001 ()29856314 (PubMedID)
Available from: 2018-07-25 Created: 2018-07-25 Last updated: 2022-03-23Bibliographically approved
Zivanov, J., Nakane, T., Forsberg, B. O., Kimanius, D., Hagen, W. J. H., Lindahl, E. & Scheres, S. H. W. (2018). New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLIFE, 7, Article ID e42166.
Open this publication in new window or tab >>New tools for automated high-resolution cryo-EM structure determination in RELION-3
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2018 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 7, article id e42166Article in journal (Refereed) Published
Abstract [en]

Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 angstrom compared to previous RELION versions.

National Category
Biological Sciences
Research subject
Biochemistry towards Bioinformatics
Identifiers
urn:nbn:se:su:diva-162855 (URN)10.7554/eLife.42166 (DOI)000450857100001 ()30412051 (PubMedID)
Available from: 2018-12-28 Created: 2018-12-28 Last updated: 2022-03-23Bibliographically approved
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-0462-6540

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