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Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data
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Number of Authors: 82021 (English)In: Progress in Biophysics and Molecular Biology, ISSN 0079-6107, E-ISSN 1873-1732, Vol. 160, p. 43-52Article, review/survey (Refereed) Published
Abstract [en]

Technological advances in transmission electron microscopes and detectors have turned cryogenic electron microscopy (cryo-EM) into an essential tool for structural biology. A commonly used cryo-EM data analysis method, single particle analysis, averages hundreds of thousands of low-dose images of individual macromolecular complexes to determine a density map of the complex. The presence of symmetry in the complex is beneficial since each projection image can be assigned to multiple views of the complex. However, data processing that applies symmetry can average out asymmetric features and consequently data analysis methods are required to resolve asymmetric structural features. Scipion is a cryo-EM image processing framework that integrates functions from different image processing packages as plugins. To extend its functionality for handling symmetry mismatches, we present here a Scipion plugin termed LocalRec implementing the localized reconstruction method. When tested on an adenovirus data set, the plugin enables resolving the symmetry-mismatched trimeric fibre bound to the five-fold vertices of the capsid. Furthermore, it improves the structure determination of the icosahedral capsid by dealing with the defocus gradient across the particle. LocalRec is expected to be widely applicable in a range of cryo-EM investigations of flexible and symmetry mismatched complexes.

Place, publisher, year, edition, pages
2021. Vol. 160, p. 43-52
Keywords [en]
Cryo-EM, Single-particle analysis, Asymmetric reconstruction, Symmetry mismatch, Symmetry relaxation, Localized reconstruction
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-193808DOI: 10.1016/j.pbiomolbio.2020.05.004ISI: 000632013800007PubMedID: 32470354OAI: oai:DiVA.org:su-193808DiVA, id: diva2:1562143
Available from: 2021-06-08 Created: 2021-06-08 Last updated: 2022-02-25Bibliographically approved

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Abrishami, VahidIlca, Serban L.Gomez-Blanco, JosueRissanen, Ilonade La Rosa-Trevin, José MiguelHuiskonen, Juha T.

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Abrishami, VahidIlca, Serban L.Gomez-Blanco, JosueRissanen, Ilonade La Rosa-Trevin, José MiguelHuiskonen, Juha T.
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Department of Biochemistry and BiophysicsScience for Life Laboratory (SciLifeLab)
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