Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Architecture of the chloroplast PSI–NDH supercomplex in Hordeum vulgare

Abstract

The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET)1,2,3. The NDH complex associates with PSI to form the PSI–NDH supercomplex and fulfil its function. Here, we report cryo-electron microscopy structures of a PSI–NDH supercomplex from barley (Hordeum vulgare). The structures reveal that PSI–NDH is composed of two copies of the PSI–light-harvesting complex I (LHCI) subcomplex and one NDH complex. Two monomeric LHCI proteins, Lhca5 and Lhca6, mediate the binding of two PSI complexes to NDH. Ten plant chloroplast-specific NDH subunits are presented and their exact positions as well as their interactions with other subunits in NDH are elucidated. In all, this study provides a structural basis for further investigations on the functions and regulation of PSI–NDH-dependent CET.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Fig. 1: Overall architecture of the PSI–NDH supercomplex of barley.
Fig. 2: Structures of Lhca5 and Lhca6 from the PSI–LHCI-1 and PSI–LHCI-2 complexes.
Fig. 3: Structure of the NDH complex from barley.
Fig. 4: Interactions between PSI–LHCI and NDH and a functional model for PSI–NDH-mediated CET.

Data availability

The cryo-EM density map and atomic models have been deposited in the Electron Microscopy Data Bank and the Protein Data Bank for the PSI–NDH supercomplex structure at 4.4-Å resolution (EMDB ID code 31498 and PDB ID code 7F9O), the PSI–LHCI-1 supercomplex structure at 3.40-Å resolution (EMDB ID code 31348 and PDB ID code 7EW6), the PSI–LHCI-2 supercomplex structure at 3.88-Å resolution (EMDB ID code 31350 and PDB ID code 7EWK) and the NDH supercomplex structure at 3.70-Å resolution (EMDB ID code 31307 and PDB ID code 7EU3). For gel source images and mass spectrometry data, see the Supplementary Information. Source data are provided with this paper.

References

  1. Shikanai, T. Central role of cyclic electron transport around photosystem I in the regulation of photosynthesis. Curr. Opin. Biotech. 26, 25–30 (2014).

    CAS  PubMed  Google Scholar 

  2. Yamori, W. & Shikanai, T. Physiological functions of cyclic electron transport around photosystem I in sustaining photosynthesis and plant growth. Annu. Rev. Plant Biol. 67, 81–106 (2016).

    CAS  PubMed  Google Scholar 

  3. Shikanai, T. Regulation of photosynthesis by cyclic electron transport around photosystem I. Adv. Bot. Res. 96, 177–204 (2020).

    CAS  Google Scholar 

  4. Munekage, Y. et al. Cyclic electron flow around photosystem I is essential for photosynthesis. Nature 429, 579–582 (2004).

    ADS  CAS  PubMed  Google Scholar 

  5. Johnson, G. N. Physiology of PSI cyclic electron transport in higher plants. Biochim. Biophys. Acta 1807, 384–389 (2011).

    CAS  PubMed  Google Scholar 

  6. Miyake, C. Alternative electron flows (water-water cycle and cyclic electron flow around PSI) in photosynthesis: molecular mechanisms and physiological functions. Plant Cell Physiol. 51, 1951–1963 (2010).

    CAS  PubMed  Google Scholar 

  7. Munekage, Y. et al. PGR5 is involved in cyclic electron flow around photosystem I and is essential for photoprotection in Arabidopsis. Cell 110, 361–371 (2002).

    CAS  PubMed  Google Scholar 

  8. DalCorso, G. et al. A complex containing PGRL1 and PGR5 is involved in the switch between linear and cyclic electron flow in Arabidopsis. Cell 132, 273–285 (2008).

    CAS  PubMed  Google Scholar 

  9. Shikanai, T. et al. Directed disruption of the tobacco ndhB gene impairs cyclic electron flow around photosystem I. Proc. Natl Acad. Sci. USA 95, 9705–9709 (1998).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  10. Burrows, P. A., Sazanov, L. A., Svab, Z., Maliga, P. & Nixon, P. J. Identification of a functional respiratory complex in chloroplasts through analysis of tobacco mutants containing disrupted plastid ndh genes. EMBO J. 17, 868–876 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Kofer, W., Koop, H. U., Wanner, G. & Steinmüller, K. Mutagenesis of the genes encoding subunits A, C, H, I, J and K of the plastid NAD(P)H-plastoquinone-oxidoreductase in tobacco by polyethylene glycol-mediated plastome transformation. Mol. Gen. Genet. 258, 166–173 (1998).

    CAS  PubMed  Google Scholar 

  12. Shikanai, T. Chrloroplast NDH: a different enzyme with a structure similar to that of respiratory NADH dehydrogenase. Biochim. Biophys. Acta 1857, 1015–1022 (2016).

    CAS  PubMed  Google Scholar 

  13. Peltier, G., Aro, E.-M. & Shikanai, T. NDH-1 and NDH-2 plastoquinone reductases in oxygenic photosynthesis. Annu. Rev. Plant Biol. 67, 55–80 (2016).

    CAS  PubMed  Google Scholar 

  14. Peng, L., Shimizu, H. & Shikanai, T. The chloroplast NAD(P)H dehydrogenase complex interacts with photosystem I in Arabidopsis. J. Biol. Chem. 283, 34873–34879 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Peng, L., Fukao, Y., Fujiwara, M., Takami, T. & Shikanai, T. Efficient operation of NAD(P)H dehydrogenase requires the supercomplex formation with photosystem I via minor LHCI in Arabidopsis. Plant Cell 21, 3623–3640 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Peng, L. & Shikanai, T. Supercomplex formation with photosystem I is required for the stabilization of the chloroplast NADH dehydrogenase-like complex in Arabidopsis. Plant Physiol. 155, 1629–1639 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Kouřil, R. et al. Structural characterization of a plant photosystem I and NAD(P)H dehydrogenase supercomplex. Plant J. 77, 568–576 (2014).

    PubMed  Google Scholar 

  18. Otani, T., Kato, Y. & Shikanai, T. Specific substitutions of light-harvesting complex I proteins associated with photosystem I are required for supercomplex formation with chloroplast NADH dehydrogenase-like complex. Plant J. 94, 122–130 (2018).

    CAS  PubMed  Google Scholar 

  19. 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).

    ADS  CAS  PubMed  Google Scholar 

  20. 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).

    CAS  PubMed  Google Scholar 

  21. Wang, J. et al. Structure of plant photosystem I–light harvesting complex I supercomplex at 2.4 Å resolution. J. Integr. Plant Biol. 63, 1367–1381 (2021).

    CAS  PubMed  Google Scholar 

  22. Laughlin, T. G., Bayne, A. N., Trempe, J. F., Savage, D. F. & Davies, K. M. Structure of the complex I-like molecule NDH of oxygenic photosynthesis. Nature 566, 411–414 (2019).

    ADS  PubMed  Google Scholar 

  23. Schuller, J. M. et al. Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer. Science 363, 257–260 (2019).

    ADS  CAS  PubMed  Google Scholar 

  24. Pan, X. et al. Structural basis for electron transport mechanism of complex I-like photosynthetic NAD(P)H dehydrogenase. Nat. Commun.11, 610 (2020).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  25. Zhang, C. et al. Structural insights into NDH-1 mediated cyclic electron transfer. Nat. Commun.11, 888 (2020).

    ADS  PubMed  PubMed Central  Google Scholar 

  26. Pan, X. et al. Structure of the maize photosystem I supercomplex with light-harvesting complexes I and II. Science 360, 1109–1113 (2018).

    ADS  CAS  PubMed  Google Scholar 

  27. Shimizu, H. et al. CRR23/NdhL is a subunit of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis. Plant Cell Physiol. 49, 835–842 (2008).

    CAS  PubMed  Google Scholar 

  28. Yamamoto, H., Sato, N. & Shikanai, T. Critical role of NdhA in the incorporation of the peripheral arm into the membrane-embedded part of the chloroplast NADH dehydrogenase-like complex. Plant Cell Physiol. 62, 1131–1145 (2021).

    PubMed  Google Scholar 

  29. Ishikawa, N. et al. NDF6: a thylakoid protein specific to terrestrial plants is essential for activity of chloroplastic NAD(P)H dehydrogenase in Arabidopsis. Plant Cell Physiol. 49, 1066–1073 (2008).

    CAS  PubMed  Google Scholar 

  30. Yabuta, S. et al. Three PsbQ-like proteins are required for the function of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis. Plant Cell Physiol. 51, 866–876 (2010).

    CAS  PubMed  Google Scholar 

  31. Yamamoto, H., Peng, L., Fukao, Y. & Shikanai, T. An Src homology 3 domain-like fold protein forms a ferredoxin binding site for the chloroplast NADH dehydrogenase-like complex in Arabidopsis. Plant Cell 23, 1480–1493 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Sirpio, S. et al. Novel nuclear-encoded subunits of the chloroplast NAD(P)H dehydrogenase complex. J. Biol. Chem. 284, 905–912 (2009).

    PubMed  Google Scholar 

  33. Takabayashi, A. et al. Three novel subunits of Arabidopsis chloroplastic NAD(P)H dehydrogenase identified by bioinformatic and reverse genetic approaches. Plant J. 57, 207–219 (2009).

    CAS  PubMed  Google Scholar 

  34. Ishihara, S. et al. Distinct functions for the two PsbP-like proteins PPL1 and PPL2 in the chloroplast thylakoid lumen of Arabidopsis. Plant Physiol. 145, 668–679 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Suorsa, M. et al. Two proteins homologous to PsbQ are novel subunits of the chloroplast NAD(P)H dehydrogenase. Plant Cell Physiol. 51, 877–883 (2010).

    CAS  PubMed  Google Scholar 

  36. Kato, Y., Sugimoto, K. & Shikanai, T. NDH–PSI supercomplex assembly precedes full assembly of the NDH complex in chloroplast. Plant Physiol. 176, 1728–1738 (2018).

    CAS  PubMed  Google Scholar 

  37. Kato, Y., Odahara, M. & Shikanai, T. Evolution of an assembly factor-based subunit contributed to a novel NDH–PSI supercomplex formation in chloroplasts. Nat. Commun.12, 3685 (2021).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  38. Sirpiö, S., Holmström, M., Battchikova, N. & Aro, E. M. AtCYP20-2 is an auxiliary protein of the chloroplast NAD(P)H dehydrogenase complex. FEBS Lett. 583, 2355–2358 (2009).

    PubMed  Google Scholar 

  39. Otani, T., Yamamoto, H. & Shikanai, T. Stromal loop of Lhca6 is responsible for the linker function required for the NDH–PSI supercomplex formation. Plant Cell Physiol. 58, 851–861 (2017).

    CAS  PubMed  Google Scholar 

  40. Quiles, M. J., Albacete, M. E., Sabater, B. & Cuello, J. Isolation and partial characterization of the NADH dehydrogenase complex from barley chloroplast thylakoids. Plant Cell Physiol. 37, 1134–1142 (1996).

    Google Scholar 

  41. Ikeuchi, M. & Inoue, Y. A new 4.8-kDa polypeptide intrinsic to the PS II reaction center, as revealed by modified SDS–PAGE with improved resolution of low-molecular-weight proteins. Plant Cell Physiol. 29, 1233–1239 (1988).

    CAS  Google Scholar 

  42. Manaresi, E. et al. Chemiluminescence western blot assay for the detection of immunity against parvovirus B19 VP1 and VP2 linear epitopes using a videocamera based luminograph. J. Virol. Methods 81, 91–99 (1999).

    CAS  PubMed  Google Scholar 

  43. Schorb, M., Haberbosch, I., Hagen, W. J., Schwab, Y. & Mastronarde, D. N. Software tools for automated transmission electron microscopy. Nat. Methods 16, 471–477 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. 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 

  45. Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    CAS  PubMed  Google Scholar 

  46. Grigorieff, N. & Harrison, S. C. Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy. Curr. Opin. Struct. Biol. 21, 265–273 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  48. 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 

  49. Biasini, M. et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 42, W252–W258 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank C. Ma from the Protein Facility (School of Medicine, Zhejiang University) for providing the platform for sample purification, X. Meng in the Center of Biomedical Analysis (Tsinghua University) for protein mass spectrometry analysis and W. Tang from the Institute of Botany (CAS) for instrumental support in sample preparation. The project was funded by the National Key R&D Program of China (2020YFA0907600, 2018YFA0507700, 2017YFA0503700, 2017YFA0504803, 2019YFA0906300, 2021YFA1300403), the Strategic Priority Research Program of CAS (XDA26050402, XDB17000000), the Key Research Program of Frontier Sciences of CAS (QYZDY-SSW-SMC003), the Youth Innovation Promotion Association of CAS (2020081), the CAS Interdisciplinary Innovation Team (JCTD-2020-06), the CAS Project for Young Scientists in Basic Research (YSBR-004), the Fundamental Research Funds for the Central Universities (2018XZZX001–13) and JSPS KAKENHI (JP17H06434).

Author information

Authors and Affiliations

Authors

Contributions

X.Z., J.-R.S. and G.H. conceived the project. L.S., Z.M. and G.H. performed the sample preparation and characterization. K.T., C.W., S.C. and S.A. collected the cryo-EM data. X.Z., S.C. and H.W. processed the cryo-EM data and reconstructed the cryo-EM density map. L.S., K.T. and H.W. prepared figures. W.W. built the structure model and refined the structure. L.S., W.W., G.H., J.-R.S. and X.Z. analysed the structure. L.S., K.T., W.W., T.K., G.H., J.-R.S. and X.Z. jointly wrote the manuscript. All authors discussed and commented on the results and the manuscript.

Corresponding authors

Correspondence to Jian-Ren Shen, Guangye Han or Xing Zhang.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review informationNature thanks Roman Kouril, Toshiharu Shikanai and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 Sample preparation and characterization of the PSI-NDH supercomplex from barely.

a, Separation of the PSI-NDH supercomplex by sucrose density gradient (SDG) centrifugation from barley thylakoids. The band of PSI-NDH was indicated by a black arrow. b, Size-exclusion chromatographic elution profile of the PSI-NDH fraction isolated by SDG with a Superose 6 Increase 10/300 GL column (flow rate: 100 μl min-1) performed at 4 °C and monitored by absorption at 280 nm. c, Room-temperature absorption spectrum of the PSI-NDH obtained from the size-exclusion chromatography. For comparison, the spectrum of PSI-LHCI was also shown. The spectra were normalized based on the absorption maximum at 680 nm (indicated by a black arrow). The absorption value at 280 nm (indicated by a red arrow) of PSI-NDH is higher than that of PSI-LHCI, indicating a larger ratio of protein to chlorophylls (Chls) in PSI-NDH than that in PSI-LHCI. d, SDS-PAGE analysis of the thylakoid membrane and purified PSI-NDH from barley (For gel source data, see Supplementary Figure 1). Lane 1: marker; lane 2: thylakoid membranes; lane 3: PSI-NDH after size-exclusion chromatography. Samples were loaded onto lane 2 and lane 3 at 20 μg of Chl per lane. The bands were stained by Coomassie Brilliant Blue (CBB). e, Silver staining profiles of the SDS-PAGE gel of the purified PSI-NDH from barley. Lane 1: marker; lane 2 and lane 3: PSI-NDH after size-exclusion chromatography loaded at 20 μg and 10 μg of Chl, respectively. The proteins of the CBB and silver staining bands in panels d and e were identified based on mass spectrometry analysis (see Source Data files 1 and 2) and labeled on the right side. f, Western-blotting analysis of thylakoid membrane and PSI-NDH supercomplex using the antibodies against NdhB and PnsB5. The polypeptide samples were separated by SDS-PAGE and stained with CBB (left), and polypeptides in the gels were electrophoretically transferred to a polyvinylidene fluoride membrane and detected with antibodies against NdhB (middle) or PnsB5 (right). Lane 1: pre-stained marker; lane 2: thylakoid membrane; lane 3: PSI-NDH after size-exclusion chromatography; lane 4: unstained marker. Samples were loaded onto SDS-PAGE at 5 μg of Chl per lane. The primary antibody against PnsB5 was custom-made by Genscript, and the primary antibody against NdhB (AS164064) and the horseradish peroxidase (HRP)-conjugated secondary antibody (Goat Anti Rabbit IgG) (AS09602) were purchased from Agrisera. Data shown in this figure is repeated more than three times, and all resulted in the same results.

Source data

Extended Data Fig. 2 Data collection and image processing.

a, Flow chart of the cryo-EM data processing of the overall PSI-NDH supercomplex and local-refinement of PSI-LHCI-1, PSI-LHCI-2 and NDH sub-complexes from the four datasets (dataset 1–4). All data were collected on a K2 summit direct electron detector. b, Gold standard FSC curves of the final 3D reconstruction of the PSI-NDH supercomplex. c, Local resolution distributions of PSI-NDH generated with Relion.

Extended Data Fig. 3 Cryo-EM density maps of protein subunits and typical cofactors in the PSI-NDH supercomplex of barley.

The protein subunits are shown as cartoon and colored differently as indicated. The locations of each subunit in the supercomplex are depicted in the surface representations above each subunit. Carotenoids and lipids are represented by sticks, and the cryo-EM density maps of each subunit and cofactors are depicted in gray meshes.

Extended Data Fig. 4 Comparisons of the structure of the PSI-LHCI moieties from the barley PSI-NDH supercomplex with PSI-LHCI from pea and maize with top views from the stromal side.

a, b, Structural comparisons of barley PSI-LHCI-1 (blue) with pea PSI-LHCI (purple, PDB code: 4XK8) (a) and maize PSI-LHCI-LHCII (cyan, PDB code: 5ZJI) (b). Structural differences in the C-terminal region of Lhca1 are highlighted with black dashed boxes, and enlarged in the right side. c, d, Pigment comparisons of barley PSI-LHCI-1 (blue) with pea PSI-LHCI (purple, PDB code: 4XK8) (c) and maize PSI-LHCI-LHCII (cyan, PDB code: 5ZJI) (d). e, f, Structural comparisons of barley PSI-LHCI-2 (green) with pea PSI-LHCI (purple, PDB ID: 4XK8) (e) and maize PSI-LHCI-LHCII (cyan, PDB code: 5ZJI) (f). Structural differences in the C-terminal region of Lhca1 and the AC loop region of Lhca2/Lhca6 are highlighted with black dashed boxes, and enlarged in the right side. g, h, Pigment comparisons of barley PSI-LHCI-2 (green) with pea PSI-LHCI (purple, PDB ID: 4XK8) (g) and maize PSI-LHCI-LHCII (cyan, PDB code: 5ZJI) (h). The protein subunits are shown as ribbon models and pigments are shown as sticks in a-h. For clarity, the phytol tails of the Chls are omitted. The pigments with different arrangements between the different structures and the pigments bound to the pea or maize subunits but are missed in the barley PSI in (c), (d), (g), (h) are highlighted with black and red dashed cycles, respectively.

Extended Data Fig. 5 Structural comparisons of Lhca5 and Lhca6 from barely with Lhca4 and Lhca2 of pea and maize.

a, Comparisons of Lhca5 from barley PSI-NDH (green) with Lhca4 from pea PSI-LHCI (PDB code: 4XK8, purple) and maize PSI-LHCI (PDB code: 5ZJI, cyan). b, Comparisons of Lhca6 from barley PSI-NDH (red) with Lhca2 from pea PSI-LHCI (PDB code: 4XK8, purple) and maize PSI-LHCI (PDB code: 5ZJI, cyan). The Lhcas are shown with ribbon models, whereas the pigments and lipids are shown as sticks and colored as that of the protein subunits respectively. Different regions between the three homologues subunits are highlighted by black dashed boxes. The phytol chains of all Chls were omitted for clarity.

Extended Data Fig. 6 Multiple sequence alignments of Lhca5/Lhca6 from barley (Hordeum vulgare) with Lhca4/Lhca2 from pea (Pisum sativum) and maize (Zea mays).

a, Sequence alignment of Lhca5 from barley with Lhca4 from pea (PS) and maize (ZM). b, Sequence alignment of Lhca6 from barley with Lhca2 from pea (PS) and maize (ZM). Secondary structures are shown above the sequences. The AC loop involved in the interactions within NDH is marked with red solid line underneath the sequences in b.

Extended Data Fig. 7 Structural comparisons of NDH and its typical subunits from barley (Hordeum vulgare) with those of NDH-1L of the thermophilic cyanobacterium T. elongatus.

a, Structural comparison between the NDH moiety of PSI-NDH and the cyanobacterial NDH-1L (PDB ID: 6L7O). b-h, Structural comparisons of the typical subunits NdhA (b), NdhB (d), NdhC (e), NdhD (f), NdhF (g), and NdhG (h) between barley and T. elongatus (PDB ID: 6L7O). The structural differences between two homologues subunits are highlighted by black dashed boxes. The electron density map of the N-terminal loop of NdhA of barley and its interactions with the surface of PnsL2 is shown in (c). i, Structural comparison between PnsB4 of barley and NdhP of T. elongatus (PDB ID: 6L7O). The extra extensions of the C-terminus and N-terminus found in PnsB4 were highlighted by black dashed boxes. In all panels, subunits in barley NDH are shown in same color as in Fig. 3a, and subunits in the cyanobacterial NDH-1L are shown in grey.

Extended Data Fig. 8 Interactions among different subunits in NDH.

a, Interactions between the PnsB4 helix inserted inside PnsB1 with PnsB5. b, Interactions between PnsL3 and NdhF mediated through the N-terminal region of PnsB4, and interactions between the N-terminal region of PnsL3 with NdhD. c, Interactions between the transmembrane regions of PnsB5 with PnsB4. The NdhB/D/F subunits are shown in the surface model. d, Interactions of the long N-terminal loop of PnsB5 with NdhD and NdhF. e, Interactions between PnsB1 and the horizontal helix of NdhF in the stromal side. f, Interactions of PnsL4 with PnsL1 and PnsL2 mediated through the lumenal helices of NdhG. The lumenal helices of NdhG are shown in surface model. g, Interactions of PnsL2 with NdhA, NdhB, NdhC, NdhE, NdhG and PnsL4. h, Interactions of PnsL5 with PnsL4, NdhB and NdhD. i, Interactions between NdhF loopTM13-TM14 and PnsB2, PnsB3. j, Interactions between NdhF loopTM15-TM16 and PnsB2 as well as between the NdhF horizontal helix and PnsB3.

Extended Data Fig. 9 Structures of the plant-chloroplast-specific (PCS)-subunits PnsB3, PnsL1, PnsL2 and PnsL3 of NDH from barley (Hordeum vulgare), and sequence alignments of PnsL1/PnsL2/PnsL3 from barley (HV) NDH with PsbP/PsbQ from Spinacia oleracea (SO).

a, The structure of barley PnsB3. The Fe-S cluster and four coordinated cysteine residues are shown in ball-and-sticks. b, The local environment of the Fe-S cluster of PnsB3 in the NDH complex. c, Superposition of the barley PnsL1 and spinach PsbP structures (PDB ID: 3JCU). d, Superposition of the barley PnsL2 and spinach PsbQ structures (PDB ID: 3JCU). e, Superposition of the barley PnsL3 and spinach PsbQ structures (PDB ID: 3JCU). f, Sequence alignment of PnsL1 with spinach PsbP. g, Sequence alignment of PnsL2 with spinach PsbQ. h, Sequence alignment of PnsL3 with spinach PsbQ.

Extended Data Fig. 10 Structure and localization of USP in the barley PSI-NDH supercomplex.

a, Surface representation of the PSI-NDH supercomplex structure. The regions involving USP are highlighted by a red dashed box and a black box, and enlarged in the middle of the figure. USP is located at the surface of membrane subunits NdhB, NdhE, NdhF and NdhG, and connected to the PnsB1 subunit. Interactions between the C-terminus of USP and Lhca5 are depicted in the right side of the panel. b, Western-blotting analysis of thylakoid membrane and PSI-NDH supercomplex using the antibody against PGR5 and PGRL1 (see Supplementary Fig. 2 for gel source data). The polypeptide samples were separated by SDS-PAGE and stained with CBB (left), and detected with antibodies against PGR5 (middle) and PGRL1 (right). Lane 1: pre-stained marker; lane 2: thylakoid membrane; lane 3: PSI-NDH after size-exclusion chromatography; lane 4: unstained marker. Samples of 5 μg of Chl were loaded per lane. Data shown in this figure is repeated more than three times, and all resulted in the same results.

Extended Data Table 1 Cryo-EM data collection and processing statistics, and list of PSI-NDH subunits identified in barley in the present study
Extended Data Table 2 Cofactors associated with each subunit of PSI-NDH from barley identified in the present study

Supplementary information

Supplementary Information

This file contains Supplementary Discussion, Supplementary Figs. 1 and 2, and supplementary references.

Reporting Summary

Source Data Extended Data Fig. 1

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Shen, L., Tang, K., Wang, W. et al. Architecture of the chloroplast PSI–NDH supercomplex in Hordeum vulgare. Nature 601, 649–654 (2022). https://doi.org/10.1038/s41586-021-04277-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41586-021-04277-6

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing