Abstract
Euglenophyta is a representative phylum of green-lineage secondary endosymbiotic eukaryotes. These organisms have evolved far-red light-harvesting complexes (LHCs) composed of diadinoxanthin and chlorophyll a/b, which are now classified as the LHCE family. Here we report a 2.35-Å cryo-electron microscopy structure of photosystem I (PSI) supercomplex from Euglena gracilis, with all subunits and their paralogs assigned. This structure reveals a minimal PSI core associated with twelve LHCE and four LHCII subunits. Most LHCE subunits are organized into dimers through a helix C–to–helix C interaction. Two dimers, together with a monomeric LhcE8, assemble into a (2 + 2 + 1)-type LHCE pentamer. The red-shifted pairs in the two LhcE6 subunits likely contribute to far-red absorption. The LHCII subunits form a distinct heterodimer and associate with the PsaF side. Overall, these results provide a structural basis for understanding energy transfer and dissipation, antenna subunit assembly, and far-red light-harvesting strategies in green-lineage secondary endosymbiotic organisms.
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Data availability
The composite cryo-EM map and atomic coordinates for the PSI–LHCE–LHCII supercomplex have been deposited in the Electron Microscopy Data Bank under accession code EMD-63994 and the Protein Data Bank under accession code 9UAS. The atomic coordinates data used in this study are available in the Protein Data Bank database under the accession codes 1JB0, 5ZGB, 6IJO, 6LY5, 7DKZ, 7DR2, 7DZ7, 7KSQ, 7XQP, 7Y5E, 7Y7B, 8JW0, 9JJ8, 9KC5. Source data for Supplementary Fig. 1 are provided in the Source data file. Source data are provided with this paper.
Code availability
The Python script used for the calculation of FRET rates is available at [https://doi.org/10.5281/zenodo.3250649]46,47.
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Acknowledgements
We thank X. Li from Westlake University, J.-R. Shen from Okayama University, A. Amunts from the University of Münster, and J. Yang from Shandong University for valuable discussions and advice on this project. We thank W. Wang Lab from the Institute of Botany, CAS, for providing equipment for purification, Y. Yin and D. Liu from the Institute of Botany, CAS, for technical assistance in sample characterization. We thank S. Zhang from the Southern University of Science and Technology and L. Shen from the Institute of Botany, CAS, for the valuable suggestions on the purification of PSI supercomplex. We thank L. Huang, M. Zhang and Z. Liu from the cryo-EM Facility of Westlake University for providing support with data collection, HPC Center of Westlake University for computational resources and the Mass Spectrometry & Metabolomics Core Facility of Westlake University for protein identification MS analysis. This work was supported by the National Key R&D Program of China (2025YFA0921100), the National Natural Science Foundation of China (32500203, T25B2009), Zhejiang Key Laboratory of Low-Carbon Intelligent Synthetic Biology (2024ZY01025), Westlake Research Center for Industries of the Future (WU2023C002), and the Westlake Center for Genome Editing.
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Y.F. conceived the project. Y.F. purified the proteins, performed data collection and structure determination, carried out model building and biochemical analysis, and wrote the manuscript. T.C., B.S., X.B., K.G. and P.Y. assisted with protein sequence, pigment and model analysis. X.Z. calculated the EET pathways. All authors contributed to the analysis and the final version of the paper.
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Feng, Y., Cao, T., Su, B. et al. Cryo-EM structure of a photosystem I supercomplex from Euglena gracilis containing pentameric LHCE and dimeric LHCII. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71601-x
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DOI: https://doi.org/10.1038/s41467-026-71601-x
