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Open data
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Basic information
Entry | Database: PDB / ID: 6l7o | |||||||||
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Title | cryo-EM structure of cyanobacteria Fd-NDH-1L complex | |||||||||
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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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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 | ![]() | 820.2 KB | Display | ![]() |
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PDB format | ![]() | 654.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 0849MC ![]() 0850C ![]() 0851C ![]() 6l7pC M: map data used to model this data C: citing same article ( |
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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 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 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 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 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 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 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 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 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 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 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 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 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 Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: V5V791*PLUS |
-Protein , 6 types, 6 molecules DFGRSV
#4: Protein | Mass: 57847.504 Da / Num. of mol.: 1 / Fragment: NdhD1 / Source method: isolated from a natural source 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 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 Source: (natural) ![]() ![]() Strain: BP-1 References: UniProt: Q8DL30, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#18: Protein | ![]() Mass: 10853.959 Da / Num. of mol.: 1 / Fragment: Ferredoxin Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: BP-1 / Gene: petF1, petF / Plasmid: pET28a / Production host: ![]() ![]() ![]() |
#19: Protein | Mass: 12462.559 Da / Num. of mol.: 1 / Fragment: NdhS / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DL61 |
#20: Protein | Mass: 16016.489 Da / Num. of mol.: 1 / Fragment: NdhV Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: BP-1 / Plasmid: pET28a / Production host: ![]() ![]() ![]() |
-Sugars , 1 types, 2 molecules ![](data/chem/img/DGD.gif)
#23: Sugar |
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-Non-polymers , 7 types, 81 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/FES.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/FES.gif)
#21: Chemical | ![]() #22: Chemical | ChemComp-LHG / ![]() #24: Chemical | ChemComp-AJP / ![]() #25: Chemical | ChemComp-PQN / | ![]() #26: Chemical | ChemComp-SQD / #27: Chemical | ![]() #28: Chemical | ChemComp-FES / | ![]() |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Fd-NDH-1L complex / Type: COMPLEX / Entity ID: #1-#20 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
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
EM software | Name: RELION / Version: 3 / Category: image acquisition |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction![]() | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 338822 / Symmetry type: POINT |