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Open data
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Basic information
Entry | Database: PDB / ID: 6khi | ||||||||||||||||||||||||||||||
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Title | Supercomplex for cylic electron transport in cyanobacteria | ||||||||||||||||||||||||||||||
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![]() | ELECTRON TRANSPORT / Cylic electron transport / photosynthetic NDH complex / Cyanobacteria | ||||||||||||||||||||||||||||||
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 / NADH dehydrogenase activity / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / ubiquinone binding / NADH dehydrogenase (ubiquinone) activity / quinone binding ...: / 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 / NADH dehydrogenase activity / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / ubiquinone binding / NADH dehydrogenase (ubiquinone) activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / electron transport chain / 2 iron, 2 sulfur cluster binding / NAD binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||||||||||||||||||||||||||
![]() | Pan, X. / Cao, D. / Xie, F. / Zhang, X. / Li, M. | ||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for electron transport mechanism of complex I-like photosynthetic NAD(P)H dehydrogenase. Authors: Xiaowei Pan / Duanfang Cao / Fen Xie / Fang Xu / Xiaodong Su / Hualing Mi / Xinzheng Zhang / Mei Li / ![]() Abstract: NAD(P)H dehydrogenase-like (NDH) complex NDH-1L of cyanobacteria plays a crucial role in cyclic electron flow (CEF) around photosystem I and respiration processes. NDH-1L couples the electron ...NAD(P)H dehydrogenase-like (NDH) complex NDH-1L of cyanobacteria plays a crucial role in cyclic electron flow (CEF) around photosystem I and respiration processes. NDH-1L couples the electron transport from ferredoxin (Fd) to plastoquinone (PQ) and proton pumping from cytoplasm to the lumen that drives the ATP production. NDH-1L-dependent CEF increases the ATP/NADPH ratio, and is therefore pivotal for oxygenic phototrophs to function under stress. Here we report two structures of NDH-1L from Thermosynechococcus elongatus BP-1, in complex with one Fd and an endogenous PQ, respectively. Our structures represent the complete model of cyanobacterial NDH-1L, revealing the binding manner of NDH-1L with Fd and PQ, as well as the structural elements crucial for proper functioning of the NDH-1L complex. Together, our data provides deep insights into the electron transport from Fd to PQ, and its coupling with proton translocation in NDH-1L. | ||||||||||||||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 734.9 KB | Display | ![]() |
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PDB format | ![]() | 590.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9989MC ![]() 9990C ![]() 6khjC 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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1 |
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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, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#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, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#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, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#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, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#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, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#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, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#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, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#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, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#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, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
-Protein , 6 types, 6 molecules DFGSV1
#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, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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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, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#18: Protein | Mass: 12462.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: BP-1 / Production host: ![]() ![]() |
#19: Protein | Mass: 16016.489 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: BP-1 / Production host: ![]() ![]() |
#20: Protein | Mass: 10853.959 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: BP-1 / Gene: petF1, petF / Production host: ![]() ![]() |
-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*PLUS |
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#17: Protein/peptide | Mass: 4858.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: V5V791*PLUS |
-Sugars , 1 types, 2 molecules ![](data/chem/img/DGD.gif)
#21: Sugar |
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-Non-polymers , 6 types, 17 molecules ![](data/chem/img/LHG.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
#22: Chemical | ChemComp-LHG / #23: Chemical | #24: Chemical | #25: Chemical | #26: Chemical | #27: Chemical | ChemComp-FES / | |
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-Details
Has ligand of interest | Y |
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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: Electron transport complex NDH-Fd from cyanobacteria / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7 |
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: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152003 / Symmetry type: POINT | ||||||||||||||||||||||||
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