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TitleFlyTomo: a streamlined software for on-the-fly cryo-ET data processing and diagnosis.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateJul 28, 2026
AuthorsZheyuan Zhang / Cheng Peng / Weiping Zhang / Jiaming Liang / Kexin Liu / Yong Chen / Junxia Zhang / Rui Liang / Yutong Song / Sai Li /
PubMed AbstractCryo-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 ...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.
External linksNat Commun / PubMed:42649199 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution3.6 - 4.6 Å
Structure data

66624

9x6s

EMDB-66624: Structure of hemagglutinin from influenza A virions determined by sub-tomogram averaging
PDB-9x6s: Structure of Influenza Hemagglutinin (A/Puerto Rico/8/1934)
Method: EM (subtomogram averaging) / Resolution: 3.6 Å

66628

9x6z

EMDB-66628, PDB-9x6z:
Structure of the HCoV-229E spike glycoprotein determined by subtomogram averaging
Method: EM (subtomogram averaging) / Resolution: 3.9 Å

EMDB-66645: Structure of the vesicular stomatitis virus nucleocapsid subbox
Method: EM (subtomogram averaging) / Resolution: 4.6 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • Influenza A virus (A/ Puerto Rico/8/34 (H1N1))
  • human coronavirus 229e
  • influenza a virus (a/puerto rico/8/1934(h1n1))
KeywordsVIRAL PROTEIN / Hemagglutinin / Glycoprotein.Prefusion / Ectodomain / Spike / HCoV-229E

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