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Open data
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Basic information
Entry | Database: PDB / ID: 6nbx | ||||||||||||
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Title | T.elongatus NDH (data-set 2) | ||||||||||||
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![]() | OXIDOREDUCTASE / photosynthesis / bioenergetics / membrane protein complex | ||||||||||||
Function / homology | ![]() : / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / NADH dehydrogenase activity / ubiquinone binding / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity ...: / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / NADH dehydrogenase activity / ubiquinone binding / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / NAD binding / 4 iron, 4 sulfur cluster binding / iron ion binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
![]() | Laughlin, T.G. / Bayne, A. / Trempe, J.-F. / Savage, D.F. / Davies, K.M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the complex I-like molecule NDH of oxygenic photosynthesis. Authors: Thomas G Laughlin / Andrew N Bayne / Jean-François Trempe / David F Savage / Karen M Davies / ![]() ![]() Abstract: Cyclic electron flow around photosystem I (PSI) is a mechanism by which photosynthetic organisms balance the levels of ATP and NADPH necessary for efficient photosynthesis. NAD(P)H dehydrogenase-like ...Cyclic electron flow around photosystem I (PSI) is a mechanism by which photosynthetic organisms balance the levels of ATP and NADPH necessary for efficient photosynthesis. NAD(P)H dehydrogenase-like complex (NDH) is a key component of this pathway in most oxygenic photosynthetic organisms and is the last large photosynthetic membrane-protein complex for which the structure remains unknown. Related to the respiratory NADH dehydrogenase complex (complex I), NDH transfers electrons originating from PSI to the plastoquinone pool while pumping protons across the thylakoid membrane, thereby increasing the amount of ATP produced per NADP molecule reduced. NDH possesses 11 of the 14 core complex I subunits, as well as several oxygenic-photosynthesis-specific (OPS) subunits that are conserved from cyanobacteria to plants. However, the three core complex I subunits that are involved in accepting electrons from NAD(P)H are notably absent in NDH, and it is therefore not clear how NDH acquires and transfers electrons to plastoquinone. It is proposed that the OPS subunits-specifically NdhS-enable NDH to accept electrons from its electron donor, ferredoxin. Here we report a 3.1 Å structure of the 0.42-MDa NDH complex from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1, obtained by single-particle cryo-electron microscopy. Our maps reveal the structure and arrangement of the principal OPS subunits in the NDH complex, as well as an unexpected cofactor close to the plastoquinone-binding site in the peripheral arm. The location of the OPS subunits supports a role in electron transfer and defines two potential ferredoxin-binding sites at the apex of the peripheral arm. These results suggest that NDH could possess several electron transfer routes, which would serve to maximize plastoquinone reduction and avoid deleterious off-target chemistry of the semi-plastoquinone radical. | ||||||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 659.2 KB | Display | ![]() |
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PDB format | ![]() | 541.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 110.2 KB | Display | |
Data in CIF | ![]() | 169.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0425MC ![]() 0415C ![]() 0416C ![]() 0417C ![]() 0418C ![]() 0419C ![]() 0420C ![]() 6nbqC ![]() 6nbyC C: citing same article ( M: map data used to model this data |
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Similar structure data | |
EM raw data | ![]() Data size: 1.8 TB Data #1: Unaligned multiframe micrographs for NDH dataset1 [micrographs - multiframe] Data #2: Unaligned multiframe micrographs for NDH dataset2 [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
-NAD(P)H-quinone oxidoreductase subunit ... , 12 types, 12 molecules ABCEHIJKLMNO
#1: Protein | Mass: 40565.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DL32, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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#2: Protein | Mass: 55168.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DMR6, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#3: Protein | Mass: 15013.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DJ02, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#5: Protein | Mass: 11140.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DL29, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#8: Protein | Mass: 45271.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DJD9, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#9: Protein | Mass: 22444.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DL31, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#10: Protein | Mass: 19363.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DJ01, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#11: Protein | Mass: 25766.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DKZ4, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#12: Protein | Mass: 8575.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DKZ3, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#13: Protein | Mass: 12584.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DLN5, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#14: Protein | Mass: 16656.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DJU2, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#15: Protein | Mass: 7877.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DMU4, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
-Protein , 4 types, 4 molecules DFGS
#4: Protein | Mass: 57847.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DKY0, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
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#6: Protein | Mass: 72025.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DKX9 |
#7: Protein | Mass: 21580.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DL30, NADH dehydrogenase (quinone) |
#18: Protein | Mass: 12462.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DL61 |
-Proton-translocating NADH-quinone dehydrogenase subunit ... , 2 types, 2 molecules PQ
#16: Protein/peptide | Mass: 4878.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: V5V507 |
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#17: Protein/peptide | Mass: 4844.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 |
-Non-polymers , 1 types, 3 molecules ![](data/chem/img/SF4.gif)
#19: Chemical |
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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 |
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Sample preparation
Component | Name: NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L)from T.elongatus Type: COMPLEX / Entity ID: #1-#8, #10-#18 / Source: NATURAL | ||||||||||||||||
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Molecular weight | Value: 0.42 MDa / Experimental value: YES | ||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||
Buffer solution | pH: 6 | ||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.03 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K Details: incubate on grid for 30 seconds and blot 2.5 seconds before plunging |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1385 / Details: Three image per hole, focusing once per hole. |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 25 eV |
Image scans | Movie frames/image: 30 / Used frames/image: 1-30 |
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Processing
Software | Name: PHENIX / Version: (1.13_2998: phenix.real_space_refine) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: Super-resolution movies were aligned, exposure-weighted, and Fourier cropped to the physical pixel size. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 98145 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34655 / Algorithm: BACK PROJECTION / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 20 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Corelation coefficient | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6NBQ |