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.
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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.
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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).
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.
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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.
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.
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.
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.
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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
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