Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography

Jonathan Bouvette, Hsuan-Fu Liu, Xiaochen Du, Ye Zhou, Andrew P. Sikkema, Juliana da Fonseca Rezende e Mello, Bradley P. Klemm, Rick Huang, Roel M. Schaaper, Mario J. Borgnia () and Alberto Bartesaghi ()
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Jonathan Bouvette: National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services
Hsuan-Fu Liu: Duke University School of Medicine
Xiaochen Du: Duke University
Ye Zhou: Duke University
Andrew P. Sikkema: National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services
Juliana da Fonseca Rezende e Mello: National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services
Bradley P. Klemm: National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services
Rick Huang: Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Department of Health and Human Services
Roel M. Schaaper: National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services
Mario J. Borgnia: National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services
Alberto Bartesaghi: Duke University School of Medicine

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: Abstract Tomographic reconstruction of cryopreserved specimens imaged in an electron microscope followed by extraction and averaging of sub-volumes has been successfully used to derive atomic models of macromolecules in their biological environment. Eliminating biochemical isolation steps required by other techniques, this method opens up the cell to in-situ structural studies. However, the need to compensate for errors in targeting introduced during mechanical navigation of the specimen significantly slows down tomographic data collection thus limiting its practical value. Here, we introduce protocols for tilt-series acquisition and processing that accelerate data collection speed by up to an order of magnitude and improve map resolution compared to existing approaches. We achieve this by using beam-image shift to multiply the number of areas imaged at each stage position, by integrating geometrical constraints during imaging to achieve high precision targeting, and by performing per-tilt astigmatic CTF estimation and data-driven exposure weighting to improve final map resolution. We validated our beam image-shift electron cryo-tomography (BISECT) approach by determining the structure of a low molecular weight target (~300 kDa) at 3.6 Å resolution where density for individual side chains is clearly resolved.

Date: 2021
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DOI: 10.1038/s41467-021-22251-8

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