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Open data
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Basic information
Entry | Database: PDB / ID: 6l7p | |||||||||
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Title | cryo-EM structure of cyanobacteria NDH-1LdelV complex | |||||||||
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![]() | PHOTOSYNTHESIS / photosystem I / cyclic electron transfer | |||||||||
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: 3.6 Å | |||||||||
![]() | Zhang, C. / Shuai, J. / Wu, J. / Lei, M. | |||||||||
![]() | ![]() Title: Structural insights into NDH-1 mediated cyclic electron transfer. Authors: Chunli Zhang / Jin Shuai / Zhaoxing Ran / Jiaohong Zhao / Zhenfang Wu / Rijing Liao / Jian Wu / Weimin Ma / Ming Lei / ![]() Abstract: NDH-1 is a key component of the cyclic-electron-transfer around photosystem I (PSI CET) pathway, an important antioxidant mechanism for efficient photosynthesis. Here, we report a 3.2-Å-resolution ...NDH-1 is a key component of the cyclic-electron-transfer around photosystem I (PSI CET) pathway, an important antioxidant mechanism for efficient photosynthesis. Here, we report a 3.2-Å-resolution cryo-EM structure of the ferredoxin (Fd)-NDH-1L complex from the cyanobacterium Thermosynechococcus elongatus. The structure reveals three β-carotene and fifteen lipid molecules in the membrane arm of NDH-1L. Regulatory oxygenic photosynthesis-specific (OPS) subunits NdhV, NdhS and NdhO are close to the Fd-binding site whilst NdhL is adjacent to the plastoquinone (PQ) cavity, and they play different roles in PSI CET under high-light stress. NdhV assists in the binding of Fd to NDH-1L and accelerates PSI CET in response to short-term high-light exposure. In contrast, prolonged high-light irradiation switches on the expression and assembly of the NDH-1MS complex, which likely contains no NdhO to further accelerate PSI CET and reduce ROS production. We propose that this hierarchical mechanism is necessary for the survival of cyanobacteria in an aerobic environment. | |||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 757.9 KB | Display | ![]() |
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PDB format | ![]() | 607.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 133.8 KB | Display | |
Data in CIF | ![]() | 185.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0850MC ![]() 0849C ![]() 0851C ![]() 6l7oC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-NAD(P)H-quinone oxidoreductase subunit ... , 14 types, 14 molecules ABCEHIJKLMNOPQ
#1: Protein | Mass: 40565.984 Da / Num. of mol.: 1 / Fragment: NdhA / Source method: isolated from a natural source / Details: cell 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 / Fragment: NdhB / Source method: isolated from a natural source / Details: cell 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 / Fragment: NdhC / Source method: isolated from a natural source / Details: cell 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 / Fragment: NdhE / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DL29, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#8: Protein | Mass: 45271.184 Da / Num. of mol.: 1 / Fragment: NdhH / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DJD9, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#9: Protein | Mass: 22444.801 Da / Num. of mol.: 1 / Fragment: NdhI / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DL31, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#10: Protein | Mass: 19363.789 Da / Num. of mol.: 1 / Fragment: NdhJ / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DJ01, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#11: Protein | Mass: 25766.998 Da / Num. of mol.: 1 / Fragment: NdhK / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DKZ4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#12: Protein | Mass: 8575.137 Da / Num. of mol.: 1 / Fragment: NdhL / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DKZ3, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#13: Protein | Mass: 12584.056 Da / Num. of mol.: 1 / Fragment: NdhM / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DLN5, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#14: Protein | Mass: 16656.182 Da / Num. of mol.: 1 / Fragment: NdhN / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DJU2, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#15: Protein | Mass: 7877.076 Da / Num. of mol.: 1 / Fragment: NdhO / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DMU4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#16: Protein/peptide | Mass: 4878.649 Da / Num. of mol.: 1 / Fragment: NdhP / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: V5V507*PLUS |
#17: Protein/peptide | Mass: 4844.698 Da / Num. of mol.: 1 / Fragment: NdhQ / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: V5V791*PLUS |
-Protein , 4 types, 4 molecules DFGS
#4: Protein | Mass: 57847.504 Da / Num. of mol.: 1 / Fragment: NdhD1 / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DKY0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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#6: Protein | Mass: 72025.352 Da / Num. of mol.: 1 / Fragment: NdhF1 / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DKX9 |
#7: Protein | Mass: 21580.568 Da / Num. of mol.: 1 / Fragment: NdhG / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DL30, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#18: Protein | Mass: 12462.559 Da / Num. of mol.: 1 / Fragment: NdhS / Source method: isolated from a natural source / Details: cell Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DL61 |
-Sugars , 1 types, 2 molecules ![](data/chem/img/DGD.gif)
#21: Sugar |
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-Non-polymers , 6 types, 64 molecules ![](data/chem/img/BCR.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/AJP.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/AJP.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/SF4.gif)
#19: Chemical | #20: Chemical | ChemComp-LHG / #22: Chemical | ChemComp-AJP / #23: Chemical | ChemComp-PQN / | #24: Chemical | ChemComp-SQD / #25: Chemical | |
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-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 |
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Sample preparation
Component | Name: NDH-1LDelV / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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 |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 439946 / Symmetry type: POINT |