9X6Z

Structure of the HCoV-229E spike glycoprotein determined by subtomogram averaging

Summary for 9X6Z

• Entry DOI: 10.2210/pdb9x6z/pdb
• EMDB information: 66628
• Descriptor: Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose (2 entities in total)
• Functional Keywords: spike, hcov-229e, viral protein
• Biological source: Human coronavirus 229E
• Total number of polymer chains: 3
• Total formula weight: 400865.99

Authors

Liang, J.,Peng, C.,Li, S. (deposition date: 2025-10-16, release date: 2026-09-16)

Primary citation

Zhang, Z.,Peng, C.,Zhang, W.,Liang, J.,Liu, K.,Chen, Y.,Zhang, J.,Liang, R.,Song, Y.,Li, S.
FlyTomo: a streamlined software for on-the-fly cryo-ET data processing and diagnosis.
Nat Commun, 17:-, 2026

PubMed Abstract: Cryo-ET combined with subtomogram averaging (STA) enables the structural elucidation of macromolecular assemblies in native environments. However, their widespread adoption has been limited by the labor-intensive, expertise-dependent data processing workflow. Here we present FlyTomo, a software that streamlines data processing from frame alignment to STA with high-throughput for authentic cryo-ET scenarios. During data acquisition, FlyTomo performs real-time diagnosis, enabling prompt feedback on sample quality, microscope performance and structural features. After acquisition, it aggregates diagnostic metrics into an overview, guiding users through data review and refinement. FlyTomo also curates raw and processed data into directories to simplify data management and archiving. We validate FlyTomo across a diverse set of authentic cryo-ET samples, including purified enveloped viruses and cryo-lamellae, on multiple microscopes and cameras, achieving structures at resolutions of 3.4 to 7.3 Å. Collectively, by integrating accuracy, scalability and usability, FlyTomo reduces the technical barrier for in situ structural biology using cryo-ET.

PubMed: 42649199
DOI: 10.1038/s41467-026-75998-3

Experimental method

ELECTRON MICROSCOPY (3.9 Å)