Localized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data
| Autor: | Juha T. Huiskonen, Josué Gómez-Blanco, Vijay S. Reddy, José Miguel de la Rosa-Trevín, Ilona Rissanen, Serban L. Ilca, Vahid Abrishami, José María Carazo |
|---|---|
| Přispěvatelé: | Molecular and Integrative Biosciences Research Programme, Helsinki Institute of Life Science HiLIFE, Laboratory of Structural Biology |
| Rok vydání: | 2020 |
| Předmět: |
Models
Molecular Macromolecular Substances Protein Conformation Cryo-electron microscopy Computer science 030303 biophysics Biophysics Single particle analysis Image processing Crystallography X-Ray Adenoviridae Viral Proteins 03 medical and health sciences Image Processing Computer-Assisted Asymmetric reconstruction Databases Protein Molecular Biology Cryo-EM 0303 health sciences Data processing Cryoelectron Microscopy Single-particle analysis Single Molecule Imaging Symmetry (physics) Data set Range (mathematics) Localized reconstruction Data analysis 1182 Biochemistry cell and molecular biology Symmetry relaxation Protein Multimerization Symmetry mismatch Algorithm |
| Zdroj: | Progress in Biophysics and Molecular Biology |
| ISSN: | 0079-6107 |
| DOI: | 10.1016/j.pbiomolbio.2020.05.004 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full Text from ScienceDirect