Protocols for Subtomogram Averaging of Membrane Proteins in the Dynamo Software Package.

Details

Serval ID
serval:BIB_5B90278AB6CD
Type
Article: article from journal or magazin.
Collection
Publications
Title
Protocols for Subtomogram Averaging of Membrane Proteins in the Dynamo Software Package.
Journal
Frontiers in molecular biosciences
Author(s)
Navarro P.P., Stahlberg H., Castaño-Díez D.
ISSN
2296-889X (Print)
ISSN-L
2296-889X
Publication state
Published
Issued date
2018
Peer-reviewed
Oui
Volume
5
Pages
82
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
Cryo-electron tomography allows low-resolution three-dimensional (3D) viewing of cellular organelles and macromolecular complexes present as multiple copies within a tomogram. These structures are computationally extracted and averaged in order to obtain high-resolution 3D structures, and provide a map of their spatial distribution and interaction with their biological microenvironment. To do so, we apply the user-friendly Dynamo software package on a tomographic data set. Dynamo acts as a modular toolbox adaptable to different biological scenarios, allowing a custom designed pipeline for subtomogram averaging. Here, we use as a textbook example the mitochondrial docking site of the positive-strand RNA Flock house nodavirus (FHV) to describe how Dynamo coordinates several basic steps in the subtomogram averaging workflow. Our framework covers specific strategies to deal with additional issues in subtomogram averaging as tomographic data management, 3D surface visualization, automatic assignment of asymmetry and inherent loss of Fourier information in presence of preferential views.
Keywords
cryo-electron tomography, fourier compensation, subboxing, subtomogram averaging, viral membrane complex, workflow
Pubmed
Web of science
Open Access
Yes
Create date
09/06/2023 16:02
Last modification date
22/07/2024 11:22
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