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Peer-reviewedCC BYNature Communications

Integrative structural interactomics reveals protein organization and structure in a giant virus

  • Lars Mühlberg1,2,3,4
  • Julia Ruta2,4
  • Vasilii Mikirtumov5,6,7,8,9
  • Raymond N. Burton‐Smith10,11,12,13,14,15
  • Kazuyoshi Murata10,11,12,13,14,15
  • Mikhail Kudryashev5,7,8
  • Kenta Okamoto16,17
  • Boris Bogdanow18,19,20,4
  • Fan Liu21,22,3,4
22 affiliations
  1. 1Charité Universitätsmedizin Berlin, Berlin, Germany
  2. 2Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
  3. 3Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
  4. 4Research Group "Structural Interactomics", Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Roessle-Str. 0 325 Berlin, Germany
  5. 5In situ Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
  6. 6Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
  7. 7Institute of Medical Physics and Biophysics, Charité Universitätsmedizin Berlin, Berlin, Germany
  8. 8In situ Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 1125, Germany
  9. 9Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 1195 Berlin, Germany
  10. 10Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
  11. 11Exploratory Research Center on Life and Living System (ExCELLS), National Institutes of Natural Sciences (NINS), Okazaki, Japan
  12. 12National Institute for Physiological Sciences (NIPS), National Institute of Natural Sciences (NINS), Okazaki, Japan
  13. 13Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
  14. 14Exploratory Research Center on Life and Living System (ExCELLS), National Institutes of Natural Sciences (NINS), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
  15. 15National Institute for Physiological Sciences (NIPS), National Institute of Natural Sciences (NINS), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-88, Japan
  16. 16Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
  17. 17Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, SE-75124, Uppsala, Sweden
  18. 18Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany. [email protected]
  19. 19Institute of Virology, Charité Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany. [email protected]
  20. 20Institute of Virology, Charité Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
  21. 21Charité Universitätsmedizin Berlin, Berlin, Germany. [email protected]
  22. 22Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany. [email protected]
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Abstract

Giant viruses are large DNA viruses that infect unicellular and multicellular eukaryotes and form exceptionally large extracellular particles. (Meta)genomics and (meta)transcriptomics have provided insight into their diverse coding repertoire, but many of the proteins remain to be characterized as they lack homology with known proteins. Here, we integrate cross-linking mass spectrometry, quantitative proteomics, computational tools and cryo-EM data to characterize the protein architecture of intact melbournevirus particles. Based on this, we allocate 88 viral proteins to different virion sub-compartments and propose topologies of 25 inner membrane proteins. We assign eight components of the capsid in cryo-EM data, including proteins that tether the capsid shell to the membrane, reflecting key points in virion maturation. The data provide a valuable resource and demonstrate the power of an integrative approach to gain system-level structural insights into a poorly characterized biological system.

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Cite

BibTeXRIS
BibTeX
@article{muhlberg2026integrative,
  title = {{Integrative structural interactomics reveals protein organization and structure in a giant virus}},
  author = {Lars Mühlberg and Julia Ruta and Vasilii Mikirtumov and Raymond N. Burton‐Smith and Kazuyoshi Murata and Mikhail Kudryashev and Kenta Okamoto and Boris Bogdanow and Fan Liu},
  journal = {Nature Communications},
  year = {2026},
  month = jul,
  doi = {10.1038/s41467-026-74973-2},
  url = {https://doi.org/10.1038/s41467-026-74973-2},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Integrative structural interactomics reveals protein organization and structure in a giant virus
AU  - Lars Mühlberg
AU  - Julia Ruta
AU  - Vasilii Mikirtumov
AU  - Raymond N. Burton‐Smith
AU  - Kazuyoshi Murata
AU  - Mikhail Kudryashev
AU  - Kenta Okamoto
AU  - Boris Bogdanow
AU  - Fan Liu
PY  - 2026
DA  - 2026/07/13
JO  - Nature Communications
DO  - 10.1038/s41467-026-74973-2
UR  - https://doi.org/10.1038/s41467-026-74973-2
AB  - Giant viruses are large DNA viruses that infect unicellular and multicellular eukaryotes and form exceptionally large extracellular particles. (Meta)genomics and (meta)transcriptomics have provided insight into their diverse coding repertoire, but many of the proteins remain to be characterized as they lack homology with known proteins. Here, we integrate cross-linking mass spectrometry, quantitative proteomics, computational tools and cryo-EM data to characterize the protein architecture of intact melbournevirus particles. Based on this, we allocate 88 viral proteins to different virion sub-compartments and propose topologies of 25 inner membrane proteins. We assign eight components of the capsid in cryo-EM data, including proteins that tether the capsid shell to the membrane, reflecting key points in virion maturation. The data provide a valuable resource and demonstrate the power of an integrative approach to gain system-level structural insights into a poorly characterized biological system.
SN  - 2041-1723
ER  -