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TitleLocalized reconstruction in Scipion expedites the analysis of symmetry mismatches in cryo-EM data.
Journal, issue, pagesProg Biophys Mol Biol, Vol. 160, Page 43-52, Year 2021
Publish dateMay 26, 2020
AuthorsVahid Abrishami / Serban L Ilca / Josue Gomez-Blanco / Ilona Rissanen / José Miguel de la Rosa-Trevín / Vijay S Reddy / José-Maria Carazo / Juha T Huiskonen /
PubMed AbstractTechnological 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 ...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.
External linksProg Biophys Mol Biol / PubMed:32470354
MethodsEM (single particle)
Resolution3.1 - 7.34 Å
Structure data

EMDB-11008:
Icosahedral reconstruction of human adenovirus D26 capsid
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-11009:
Localized reconstruction of the trimeric fibre and its interactions with the penton base of human adenovirus HAdV-D26
Method: EM (single particle) / Resolution: 7.34 Å

EMDB-11010:
Localized reconstruction of human adenovirus D26 hexon type 1
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-11011:
Localized reconstruction of human adenovirus D26 hexon type 2
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-11012:
Localized reconstruction of human adenovirus D26 hexon type 3
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-11013:
Localized reconstruction of human adenovirus D26 hexon type 4
Method: EM (single particle) / Resolution: 3.1 Å

Source
  • Homo sapiens (human)

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