Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data

Vahid Abrishami, Serban L. Ilca, Josué Gómez-Blanco, Ilona Rissanen, José Miguel de la Rosa-Trevín, Vijay S Reddy, José María Carazo, Juha T. Huiskonen

Research output: Contribution to journalArticleScientificpeer-review

Abstract

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 functionalities 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.
Original languageEnglish
JournalProgress in Biophysics & Molecular Biology
Number of pages10
ISSN0079-6107
DOIs
Publication statusAccepted/In press - 26 May 2020
MoE publication typeA1 Journal article-refereed

Fields of Science

  • 1182 Biochemistry, cell and molecular biology

Cite this