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

Frontiers in Molecular Biosciences
Paula P NavarroDaniel Castaño-Díez

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.

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Citations

Jun 27, 2019·Nature Neuroscience·Sarah H ShahmoradianMatthias E Lauer
Dec 16, 2020·Journal of Structural Biology: X·Benjamin BasantaDanielle A Grotjahn
Nov 4, 2020·Nature Neuroscience·Yun-Tao LiuGuo-Qiang Bi
Oct 31, 2020·Trends in Microbiology·Tanmay A M BharatVikram Alva
Aug 19, 2021·Nature Communications·Shrawan Kumar MageswaranYi-Wei Chang
Aug 27, 2021·PLoS Biology·Stefano Scaramuzza, Daniel Castaño-Díez

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Methods Mentioned

BETA
hand draw
electron tomography

Software Mentioned

dview
grepTable
dalign
zOriented
dtmshow
particlesData
dtmlice
Chimera
dcp GUI
SliceGraphic

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