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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).

References

  1. Barber, J. Engine of life and big bang of evolution: a personal perspective. Photosynth. Res. 80, 137–155 (2004).

    Article  CAS  PubMed  Google Scholar 

  2. Nelson, N. Photosystems and global effects of oxygenic photosynthesis. Biochim. Biophys. Acta 1807, 856–863 (2011).

    Article  CAS  PubMed  Google Scholar 

  3. Bengis, C. & Nelson, N. Purification and properties of the photosystem I reaction center from chloroplasts. J. Biol. Chem. 250, 2783–2788 (1975).

    Article  CAS  PubMed  Google Scholar 

  4. Jordan, P. et al. Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution. Nature 411, 909–917 (2001).

    Article  CAS  PubMed  Google Scholar 

  5. Umena, Y., Kawakami, K., Shen, J. R. & Kamiya, N. Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 A. Nature 473, 55–60 (2011).

    Article  CAS  PubMed  Google Scholar 

  6. Mazor, Y., Borovikova, A., Caspy, I. & Nelson, N. Structure of the plant photosystem I supercomplex at 2.6 Å resolution. Nat. Plants 3, 17014 (2017).

    Article  CAS  PubMed  Google Scholar 

  7. Qin, X., Suga, M., Kuang, T. & Shen, J. R. Structural basis for energy transfer pathways in the plant PSI–LHCI supercomplex. Science 348, 989–995 (2015).

    Article  CAS  PubMed  Google Scholar 

  8. Mazor, Y., Nataf, D., Toporik, H. & Nelson, N. Crystal structures of virus-like photosystem I complexes from the mesophilic cyanobacterium Synechocystis PCC 6803. eLife 3, e01496 (2014).

    Article  PubMed Central  Google Scholar 

  9. Stroebel, D., Choquet, Y., Popot, J. L. & Picot, D. An atypical haem in the cytochrome b6f complex. Nature 426, 413–418 (2003).

    Article  CAS  PubMed  Google Scholar 

  10. Kurisu, G., Zhang, H., Smith, J. L. & Cramer, W. A. Structure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity. Science 302, 1009–1014 (2003).

    Article  CAS  PubMed  Google Scholar 

  11. Su, X. et al. Structure and assembly mechanism of plant C2S2M2-type PSII-LHCII supercomplex. Science 357, 815–820 (2017).

    Article  CAS  PubMed  Google Scholar 

  12. Nagao, R. et al. Structural basis for energy harvesting and dissipation in a diatom PSII–FCPII supercomplex. Nat. Plants 5, 890–901 (2019).

    Article  CAS  PubMed  Google Scholar 

  13. Sheng, X. et al. Structural insight into light harvesting for photosystem II in green algae. Nat. Plants 5, 1320–1330 (2019).

    Article  CAS  PubMed  Google Scholar 

  14. Ben-Shem, A., Frolow, F. & Nelson, N. The crystal structure of plant photosystem I. Nature 426, 630–635 (2003).

    Article  CAS  PubMed  Google Scholar 

  15. Fischer, N., Hippler, M., Sétif, P., Jacquot, J. P. & Rochaix, J. D. The PsaC subunit of photosystem I provides an essential lysine residue for fast electron transfer to ferredoxin. EMBO J. 17, 849–858 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Fischer, N., Sétif, P. & Rochaix, J. D. Site-directed mutagenesis of the PsaC subunit of photosystem I: Fb is the cluster interacting with soluble ferredoxin. J. Biol. Chem. 274, 23333–23340 (1999).

    Article  CAS  PubMed  Google Scholar 

  17. Barth, P., Guillouard, I., Sétif, P. & Lagoutte, B. Essential role of a single arginine of photosystem I in stabilizing the electron transfer complex with ferredoxin. J. Biol. Chem. 275, 7030–7036 (2000).

    Article  CAS  PubMed  Google Scholar 

  18. Bottin, H., Hanley, J. & Lagoutte, B. Role of acidic amino acid residues of PsaD subunit on limiting the affinity of photosystem I for ferredoxin. Biochem. Biophys. Res. Commun. 287, 833–836 (2001).

    Article  CAS  PubMed  Google Scholar 

  19. Hanley, J., Sétif, P., Bottin, H. & Lagoutte, B. Mutagenesis of photosystem I in the region of the ferredoxin cross-linking site: modifications of positively charged amino acids. Biochemistry 35, 8563–8571 (1996).

    Article  CAS  PubMed  Google Scholar 

  20. Chitnis, V. P., Jungs, Y. S., Albee, L., Golbeck, J. H. & Chitnis, P. R. Mutational analysis of photosystem I polypeptides: role of PsaD and the lysyl 106 residue in the reductase activity of the photosystem I. J. Biol. Chem. 271, 11772–11780 (1996).

    Article  CAS  PubMed  Google Scholar 

  21. Kubota-Kawai, H. et al. X-ray structure of an asymmetrical trimeric ferredoxin-photosystem I complex. Nat. Plants 4, 218–224 (2018).

    Article  CAS  PubMed  Google Scholar 

  22. Malavath, T., Caspy, I., Netzer-El, S. Y., Klaiman, D. & Nelson, N. Structure and function of wild-type and subunit-depleted photosystem I in Synechocystis. Biochim. Biophys. Acta 1859, 645–654 (2018).

    Article  CAS  Google Scholar 

  23. Kurisu, G. et al. Structure of the electron transfer complex between ferredoxin and ferredoxin-NADP+ reductase. Nat. Struct. Biol. 8, 117–121 (2001).

    Article  CAS  PubMed  Google Scholar 

  24. Dai, S. et al. Structural snapshots along the reaction pathway of ferredoxin-thioredoxin reductase. Nature 448, 92–96 (2007).

    Article  CAS  PubMed  Google Scholar 

  25. Kim, J. Y., Nakayama, M., Toyota, H., Kurisu, G. & Hase, T. Structural and mutational studies of an electron transfer complex of maize sulfite reductase and ferredoxin. J. Biochem. 160, 101–109 (2016).

    Article  CAS  PubMed  Google Scholar 

  26. Cao, P. et al. Structural basis for energy and electron transfer of the photosystem I–IsiA–flavodoxin supercomplex. Nat. Plants 6, 167–176 (2020).

    Article  CAS  PubMed  Google Scholar 

  27. Netzer-El, S. Y., Caspy, I. & Nelson, N. Crystal structure of photosystem I monomer from Synechocystis PCC 6803. Front. Plant Sci. 9, 1865 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  28. Bengis, C. & Nelson, N. Subunit structure of chloroplast photosystem I reaction center. J. Biol. Chem. 252, 4564–4569 (1977).

    Article  CAS  PubMed  Google Scholar 

  29. Hippler, M. et al. The plastocyanin binding domain of photosystem I. EMBO J. 15, 6374–6384 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Antoshvili, M., Caspy, I., Hippler, M. & Nelson, N. Structure and function of photosystem I in Cyanidioschyzon merolae. Photosynth. Res. 139, 499–508 (2019).

    Article  CAS  PubMed  Google Scholar 

  31. Sommer, F., Drepper, F. & Hippler, M. The luminal helix l of PsaB is essential for recognition of plastocyanin or cytochrome c6 and fast electron transfer to photosystem I in Chlamydomonas reinhardtii. J. Biol. Chem. 277, 6573–6581 (2002).

    Article  CAS  PubMed  Google Scholar 

  32. Finazzi, G., Sommer, F. & Hippler, M. Release of oxidized plastocyanin from photosystem I limits electron transfer between photosystem I and cytochrome b6f complex in vivo. Proc. Natl Acad. Sci. USA 102, 7031–7036 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Kuhlgert, S., Drepper, F., Fufezan, C., Sommer, F. & Hippler, M. Residues PsaB Asp612 and PsaB Glu613 of photosystem I confer pH-dependent binding of plastocyanin and cytochrome c6. Biochemistry 51, 7297–7303 (2012).

    Article  CAS  PubMed  Google Scholar 

  34. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  36. Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  37. Shkolnisky, Y. & Singer, A. Viewing directions estimation in Cryo-EM using synchronization. SIAM J. Imaging Sci. 5, 1088–1110 (2012).

    Article  Google Scholar 

  38. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Binda, C., Coda, A., Aliverti, A., Zanetti, G. & Mattevi, A. Structure of the mutant E92K of [2Fe-2S] ferredoxin I from Spinacia oleracea at 1.7 Å resolution. Acta Crystallogr. D 54, 1353–1358 (1998).

  41. Moore, J. M. et al. High-resolution solution structure of reduced French bean plastocyanin and comparison with the crystal structure of poplar plastocyanin. J. Mol. Biol. 221, 533–555 (1991).

    Article  CAS  PubMed  Google Scholar 

  42. Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D. 66, 12–21 (2010).

    Article  CAS  PubMed  Google Scholar 

  43. Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of Cryo-EM density maps. Nat. Methods 11, 63–65 (2014).

    Article  CAS  PubMed  Google Scholar 

  44. The PyMOL molecular graphics system v.1.2r3pre (Schrödinger).

  45. Pettersen, E. F. et al. UCSF chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).

    CAS  PubMed  Google Scholar 

  46. Perez Boerema, A. et al. Structure of a minimal photosystem I from a green alga. Nat. Plants 6, 321–327 (2020).

    Article  CAS  PubMed  Google Scholar 

  47. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    Article  CAS  PubMed  Google Scholar 

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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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