+Open data
-Basic information
Entry | Database: PDB / ID: 7eu3 | ||||||
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Title | Chloroplast NDH complex | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / chloroplast NAD(P)H-quinone oxidoreductase / cyclic electron transport | ||||||
Function / homology | Function and homology information Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / chloroplast thylakoid membrane / photosynthesis, light reaction / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / mitochondrial membrane / NAD binding / 4 iron, 4 sulfur cluster binding ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / chloroplast thylakoid membrane / photosynthesis, light reaction / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / mitochondrial membrane / NAD binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / iron ion binding Similarity search - Function | ||||||
Biological species | Hordeum vulgare (barley) Hordeum vulgare subsp. spontaneum (wild barley) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Wang, W.D. / Shen, L. / Tang, K. / Han, G.Y. / Zhang, X. / Shen, J.R. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2022 Title: Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare. Authors: Liangliang Shen / Kailu Tang / Wenda Wang / Chen Wang / Hangjun Wu / Zhiyuan Mao / Shaoya An / Shenghai Chang / Tingyun Kuang / Jian-Ren Shen / Guangye Han / Xing Zhang / 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). The NDH complex ...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). 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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7eu3.cif.gz | 940.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eu3.ent.gz | 757.2 KB | Display | PDB format |
PDBx/mmJSON format | 7eu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/7eu3 ftp://data.pdbj.org/pub/pdb/validation_reports/eu/7eu3 | HTTPS FTP |
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-Related structure data
Related structure data | 31307MC 7ew6C 7ewkC 7f9oC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-NAD(P)H-quinone oxidoreductase subunit ... , 13 types, 13 molecules ABCEFGHIJKLMN
#1: Protein | Mass: 38544.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) References: UniProt: P92432, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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#2: Protein | Mass: 53452.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: S4Z268, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#3: Protein | Mass: 13299.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: S4Z1L1, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#5: Protein | Mass: 11199.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) References: UniProt: A0A218LNA9, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#6: Protein | Mass: 87552.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
#7: Protein | Mass: 19587.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: A0A4Y5SEJ9, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#8: Protein | Mass: 44563.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: S4Z272, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#9: Protein | Mass: 19271.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) References: UniProt: A0A218LNN1, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#10: Protein | Mass: 18733.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
#11: Protein | Mass: 27568.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: S4Z232, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#12: Protein | Mass: 22240.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
#13: Protein | Mass: 24051.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
#14: Protein | Mass: 25928.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
-Protein , 2 types, 2 molecules DT
#4: Protein | Mass: 56222.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) References: UniProt: S4Z8N2, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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#15: Protein | Mass: 5209.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
-Photosynthetic NDH subunit of subcomplex ... , 10 types, 10 molecules 1234567890
#16: Protein | Mass: 17835.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
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#17: Protein | Mass: 23946.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
#18: Protein | Mass: 24733.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
#19: Protein | Mass: 13954.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
#20: Protein | Mass: 25818.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
#21: Protein | Mass: 51675.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
#22: Protein | Mass: 38079.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
#23: Protein | Mass: 13313.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
#24: Protein | Mass: 9756.810 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
#25: Protein | Mass: 18146.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley) |
-Non-polymers , 4 types, 5 molecules
#26: Chemical | ChemComp-LHG / | ||
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#27: Chemical | ChemComp-BCR / | ||
#28: Chemical | #29: Chemical | ChemComp-SF4 / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Chloroplast NDH complex of Barley / Type: COMPLEX / Entity ID: #1-#25 / Source: NATURAL |
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Source (natural) | Organism: Hordeum vulgare subsp. spontaneum (wild barley) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: (1.17.1_3660:phenix.real_space_refine) / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103844 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: THROUGHOUT | ||||||||||||||||||||||||
Displacement parameters | Biso max: 346.78 Å2 / Biso mean: 138.3381 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||
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