High-confidence 3D template matching for cryo-electron tomography

Sergio Cruz-León, Tomáš Majtner, Patrick C. Hoffmann, Jan Philipp Kreysing, Sebastian Kehl, Maarten W. Tuijtel, Stefan L. Schaefer, Katharina Geißler, Martin Beck (), Beata Turoňová () and Gerhard Hummer ()
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Sergio Cruz-León: Max Planck Institute of Biophysics
Tomáš Majtner: Max Planck Institute of Biophysics
Patrick C. Hoffmann: Max Planck Institute of Biophysics
Jan Philipp Kreysing: Max Planck Institute of Biophysics
Sebastian Kehl: Max Planck Computing and Data Facility
Maarten W. Tuijtel: Max Planck Institute of Biophysics
Stefan L. Schaefer: Max Planck Institute of Biophysics
Katharina Geißler: Max Planck Institute of Biophysics
Martin Beck: Max Planck Institute of Biophysics
Beata Turoňová: Max Planck Institute of Biophysics
Gerhard Hummer: Max Planck Institute of Biophysics

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract Visual proteomics attempts to build atlases of the molecular content of cells but the automated annotation of cryo electron tomograms remains challenging. Template matching (TM) and methods based on machine learning detect structural signatures of macromolecules. However, their applicability remains limited in terms of both the abundance and size of the molecular targets. Here we show that the performance of TM is greatly improved by using template-specific search parameter optimization and by including higher-resolution information. We establish a TM pipeline with systematically tuned parameters for the automated, objective and comprehensive identification of structures with confidence 10 to 100-fold above the noise level. We demonstrate high-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, fatty acid synthases, lipid membranes and microtubules, and individual subunits inside crowded eukaryotic cells. We provide software tools for the generic implementation of our method that is broadly applicable towards realizing visual proteomics.

Date: 2024
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DOI: 10.1038/s41467-024-47839-8

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