Single-particle cryo-EM structures from iDPC–STEM at near-atomic resolution

• Published in: Nature methods Vol. 19; no. 9; pp. 1126 - 1136
• Main Authors: Lazić, Ivan, Wirix, Maarten, Leidl, Max Leo, de Haas, Felix, Mann, Daniel, Beckers, Maximilian, Pechnikova, Evgeniya V., Müller-Caspary, Knut, Egoavil, Ricardo, Bosch, Eric G. T., Sachse, Carsten
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.09.2022; Nature Publishing Group
• Subjects: 631/1647/2258/1258/1259; 631/1647/2258/1258/1260; Bioinformatics; Biological Microscopy; Biological properties; Biological samples; Biological Techniques; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Cryoelectron Microscopy - methods; Data acquisition; High resolution; Image reconstruction; Keyholes; Life Sciences; Macromolecules; Micrography; Microscopes; Microscopy, Electron, Scanning Transmission; Phase contrast; Photomicrographs; Proteomics; Scanning electron microscopy; Scanning transmission electron microscopy; Tobacco; Tobamovirus; Transmission electron microscopy; Viruses
• ISSN: 1548-7091; 1548-7105; 1548-7105
• DOI: 10.1038/s41592-022-01586-0

In electron cryomicroscopy (cryo-EM), molecular images of vitrified biological samples are obtained by conventional transmission microscopy (CTEM) using large underfocuses and subsequently computationally combined into a high-resolution three-dimensional structure. Here, we apply scanning transmission electron microscopy (STEM) using the integrated differential phase contrast mode also known as iDPC–STEM to two cryo-EM test specimens, keyhole limpet hemocyanin (KLH) and tobacco mosaic virus (TMV). The micrographs show complete contrast transfer to high resolution and enable the cryo-EM structure determination for KLH at 6.5 Å resolution, as well as for TMV at 3.5 Å resolution using single-particle reconstruction methods, which share identical features with maps obtained by CTEM of a previously acquired same-sized TMV data set. These data show that STEM imaging in general, and in particular the iDPC–STEM approach, can be applied to vitrified single-particle specimens to determine near-atomic resolution cryo-EM structures of biological macromolecules. This paper explores the use of scanning transmission electron microscopy (STEM) to vitrified biological samples for biomolecular structure elucidation. Integrated differential phase contrast (iDPC)–STEM imaging of keyhole limpet hemocyanin and tobacco mosaic virus enabled cryo-EM structure determination at 6.5 and 3.5 Å resolution, respectively.