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Absolute hand determination of glycofibrils from natural sources in cryo-EM
Open accessPreprint — published as 10.1073/pnas.2531477123 · Paper page
Abstract
Glycans are one of the four fundamental macromolecules that constitute life. However, compared with proteins and nucleic acids, our understanding of the structures and functional mechanisms of glycans remains limited. Moreover, it is generally challenging to obtain high-resolution three-dimensional structures of glycans. Recent studies have demonstrated the potential of the CryoSeek strategy in enabling high-throughput structural determination of glycans, thereby presenting novel avenues for their structural investigation. Meanwhhile, unlike proteins, near atomic resolution density maps of glycofibrils do not inherently facilitate the determination of absolute hand, which is a prerequisite for building atomic models of glycofibrils. Existing absolute hand determination methods have severe limitations in the cases of glycofibrils from natural sources. In this study, we introduce Ahaha, a straightforward and efficient method for determining such absolute hand in cryo-EM. With their absolute hand measured by Ahaha, we built atomic models of four glycofibrils derived from a natural water sample, facilitating the study of glycans. The online service of Ahaha is available at https://cryoseek.org/ahaha .
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Varadi, M., Bertoni, D., Magana, P., Paramval, U., Pidruchna, I., Radhakrishnan, M., Tsenkov, M., Nair, S., Mirdita, M., Yeo, J., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad1011 · Cited by 2,052
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Metadata
- Authors
- Zhang, Q., Qin, L., Wang, T., Li, Z., Zhang, Y., Chen, S., Yan, N., Wang, J., & Hu, M.
- Affiliations
- Shenzhen Medical Academy of Research and Translation (CN)
- Center for Life Sciences (CN)
- Corresponding author
- Yan, Nieng
- Wang, Jiawei
- Hu, Mingxu
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- openRxiv
- Published
- 2025-10-02
- Volume
- 123
- Issue
- 9
- Pages
- e2531477123-e2531477123
- ISSN
- 0027-8424 (ISSN-L)
- PMC
- PMC12956863
- OpenAlex
- W7131404605
- Cited by
- 3
- References
- 1
- Citations by year
- 2026: 3
- FWCI
- 5.93
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc-nd
- www.biorxiv.org/about/FAQ#license (vor)
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- Funders
- National Natural Science Foundation of China (92478205, 32371254, 32171190)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Advanced Electron Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- glycans, cryo-electron microscopy, glycan structure, natural water samples
- MeSH terms
- Models, Molecular, Polysaccharides, Cryoelectron Microscopy
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