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The structure of a triple complex of plant photosystem I with ferredoxin and plastocyanin

Nature Plants volume 6, pages 1300–1305 (2020)Cite this article

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Abstract

The ability of photosynthetic organisms to use sunlight as a sole source of energy is endowed by two large membrane complexes—photosystem I (PSI) and photosystem II (PSII). PSI and PSII are the fundamental components of oxygenic photosynthesis, providing oxygen, food and an energy source for most living organisms on Earth. Currently, high-resolution crystal structures of these complexes from various organisms are available. The crystal structures of megadalton complexes have revealed excitation transfer and electron-transport pathways within the various complexes. PSI is defined as plastocyanin–ferredoxin oxidoreductase but a high-resolution structure of the entire triple supercomplex is not available. Here, using a new cryo-electron microscopy technique, we solve the structure of native plant PSI in complex with its electron donor plastocyanin and the electron acceptor ferredoxin. We reveal all of the contact sites and the modes of interaction between the interacting electron carriers and PSI.

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Fig. 1: Structure of the Pc–PSI–Fd high-resolution triple complex.
Fig. 2: Distances of the electron-transfer molecules in Pc–PSI–Fd.
Fig. 3: Electrostatic interactions between PSI and Fd.
Fig. 4: Electrostatic and hydrophobic interactions between PSI and Pc.

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Data availability

The atomic coordinates of the two supercomplexes have been deposited in the PDB, under accession codes 6YAC (for PSI–Fd) and 6YEZ (for Pc–PSI–Fd). The cryo-EM maps have been deposited in the Electron Microscopy Data Bank, under accession codes EMD-10746 (for PSI–Fd) and EMD-10798 (for Pc–PSI–Fd).

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Acknowledgements

We acknowledge Diamond Light Source for access and support of the cryo-EM facilities at the UK National Electron Bio-imaging Centre (eBIC) (proposal EM BI21643-4), funded by the Wellcome Trust, MRC and BBRSC. We also thank the Electron Microscopy Core Facility (EMCF) at the European Molecular Biology Laboratory (EMBL) for their support; R. Nechushtai for allocating time for data collection; and F. Weis for his technical support. We acknowledge and thank Y. Levi-Kalisman for vitrifying and performing initial screening of the samples. Molecular graphics and analyses were performed using UCSF Chimera, developed by the Resource for Biocomputing, Visualization and Informatics at the University of California, San Francisco, with support from the National Institutes of Health (NIH) P41-GM103311. This work was supported by The Israel Science Foundation (grant no. 569/17), the Joint UGC–ISF Research (grant no. 2716/17), the German–Israeli Foundation for Scientific Research and Development (GIF; grant no. G-1483-207/2018) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 723991—CRYOMATH).

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel

    Ido Caspy, Anna Borovikova-Sheinker, Daniel Klaiman & Nathan Nelson

  2. School of Mathematical Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel

    Yoel Shkolnisky

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  1. Ido Caspy
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Contributions

I.C., A.B.-S., D.K., Y.S. and N.N. performed the research. I.C., Y.S. and N.N. analysed the data. I.C., Y.S. and N.N. wrote the manuscript. All of the authors discussed, commented on and approved the final manuscript.

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Correspondence to Yoel Shkolnisky or Nathan Nelson.

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The authors declare no competing interests.

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Peer review information: Nature Plants thanks Genji Kurisu, Mei Li and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 PSI-Fd analysis.

a, A zoomed-in view on a micrograph from the manually plunged PSI-Fd preparation. b, Representing 2D classes. c, Cryo-EM data processing workflow. d, Local resolution43 of the complete PSI-Fd (left) and map cut-through (right). e, Angular distribution of PSI-Fd. f, FSC postprocessing result.

Extended Data Fig. 2 Pc-PSI-Fd analysis.

a, A zoomed-in view of a Pc-PSI-Fd micrograph. b, Representing 2D classes. c, Cryo-EM data processing workflow. d, Local resolution43 of the complete Pc-PSI-Fd (left) and map cut-through (right). e, Angular distribution of Pc-PSI-Fd. f, FSC postprocessing result.

Extended Data Fig. 3 Lhca3 chlorophyll a 614 can handily diffuse out of PSI structure due to weak binding.

a, Chlorophyll a 614 amino acid and ligands in its local environment in Lhca3. Proximal ligands include chlorophyll a 606 and β-carotene 503. Ligands are coloured green and amino acids carbons coloured orange, oxygens in red and nitrogens in blue. PSI subunits are shown as cartoon, view and colours are the same as in Fig. 1. b, Zoom in on chlorophyll a 614 shows neither it nor chlorophyll a 606 magnesium ions are coordinated by an amino acid. Chlorophyll a 614 can readily diffuse from Lhca3 after membrane solubilization (as previously reported46), while chlorophyll a 606 is covered by β-carotene 503 and lutein 502, stabilizing its binding to Lhca3 polypeptide chain. The amino acids close to chlorophyll a 606 are Gly115, Ala118 and Pro119, while Ile128, Pro129 and Thr132 are adjacent to chlorophyll a 614. c, Map density of chlorophyll a 614 from a top and side view.

Extended Data Fig. 4 PSI-Fd EM map density.

a, Two views of the ferredoxin map density shown as mesh. Carbons are coloured light-orange, oxygens in orange and nitrogens in blue. The 2Fe-2S cluster is shown as light-orange and yellow lines. b, Second view in panel A showing ferredoxin with its density map as a surface. c, Ferredoxin map shown without the polypeptide. The region enclosing the 2Fe-2S cluster (left side of the map, colored blue) shows a local resolution range of 2.5-3 Å, decreasing as we move away from the 2Fe-2S cluster into ferredoxin centre. The loosely bound region (right side, coloured green) shows a resolution range of 3-3.7 Å, decreasing as we migrate from the ferredoxin core.

Extended Data Fig. 5 Sequence alignment of the positively charged ferredoxin binding region of PSI.

The organisms used to determine amino acid alignment were Pisum sativum, Thermosynechococcus elongatus, Synechocystis sp. PCC 6803, Chlamydomonas reinhardtii, Cyanidioschyzon merolae, Euglena gracilis and Phaeodactylum tricornutum. The relevant amino acids are marked with a dark-blue rectangle. The aligned sequences were obtained using BLAST47 or the E. gracilis Whole-genome shotgun contigs sequences. a, PsaA Arg42 and Lys46. b, PsaC Ile12-Gln16, Arg19, Lys35, Ala36 and Pro59. c, PsaD Lys150 and Lys177. d, PsaE Arg70 and Arg106. e, PsaF Lys189.

Extended Data Fig. 6 Sequence alignment of the positively charged amino acids and the hydrophobic surface of the PSI plastocyanin binding region.

The organisms used to determine amino acid alignment were Pisum sativum, Thermosynechococcus elongatus, Synechocystis sp. PCC 6803, Chlamydomonas reinhardtii, Cyanidioschyzon merolae, Euglena gracilis and Phaeodactylum tricornutum. The relevant amino acids are marked with a dark-blue rectangle. The aligned sequences were obtained using BLAST47 or the E. gracilis whole-genome shotgun contigs sequences. a, PsaA Asn641, Arg654, Asp655, Trp658, Ala659, Ser662, Gln663 and Gln666. b, PsaB Asn605, Arg621, Asp622, Trp625, Leu626, Asn627, Ser629, Gln630, Asn633 and Phe638. c, PsaA and PsaB pseudo-symmetrical luminal plastocyanin binding surface. d, PsaF Lys93, Lys96, Lys100 and Lys101. e, PsaF alignment in selected eukaryotes.

Extended Data Fig. 7 PSI-Pc EM map density.

a, Two views of the plastocyanin map density shown as mesh. Carbons are coloured cyan, oxygens in red and nitrogens in blue. The Cu+ is shown as sphere. b, Plastocyanin with its density map as a surface, local resolution ranges from 2.7-3.3 Å. c, Zoom in on the EM map at the luminal domain of plastocyanin and PsaF, coloured by local resolution. Beta-sheets are apparent, seen as long strings in the plastocyanin density map.

Extended Data Fig. 8 SDS-PAGE of purified PSI, ferredoxin and plastocyanin.

PSI – dissolved PSI crystals, purified ferredoxin and plastocyanin as described in Methods section. Polypeptide composition of dissolved P. sativum PSI crystals and purified plastocyanin (Pc) and ferredoxin (Fd). Samples were solubilised overnight at room temperature in SDS solubilising buffer containing 1% mercaptoethanol. S-standards; PSI contains 3 μg chlorophyll, Fd 3 μg and Pc 3 μg.

Extended Data Fig. 9 Example of P. sativum crystals used for the PSI-Fd and Pc-PSI-Fd cryo-EM preparations.

Scale bar, 0.2 mm.

Extended Data Fig. 10 Representative cryo-EM densities.

a, Cryo-EM densities of Ferredoxin and the [2Fe-2S] cluster. b, Cryo-EM densities of Plastocyanin and its copper ion. c, Cryo-EM densities of the electron transport chain main cofactors. d, Cryo-EM densities of PsaB chlorophyll a 1222 with its coordinated water molecule and Lhca1 chlorophyll b 609. e, Exemplary cryo-EM densities of PSI carotenoids: (BCR: β-carotene; LUT: lutein; XAT: violaxanthin; ZEA: zeaxanthin). f, Illustrative cryo-EM densities of PSI lipids: (PG: phosphatidyl glycerol; LMG: monogalactosyldiacylglycerol; DGD: digalactosyldiacylglycerol).

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Caspy, I., Borovikova-Sheinker, A., Klaiman, D. et al. The structure of a triple complex of plant photosystem I with ferredoxin and plastocyanin. Nat. Plants 6, 1300–1305 (2020). https://doi.org/10.1038/s41477-020-00779-9

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