+Open data
-Basic information
Entry | Database: PDB / ID: 6l7p | |||||||||
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Title | cryo-EM structure of cyanobacteria NDH-1LdelV complex | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / photosystem I / cyclic electron transfer | |||||||||
Function / homology | Function and homology information 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 (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / NAD binding / 4 iron, 4 sulfur cluster 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 / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / NAD binding / 4 iron, 4 sulfur cluster binding / iron ion binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Thermosynechococcus elongatus BP-1 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Zhang, C. / Shuai, J. / Wu, J. / Lei, M. | |||||||||
Citation | Journal: Nat Commun / Year: 2020 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. | |||||||||
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 | 6l7p.cif.gz | 746 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l7p.ent.gz | 619.3 KB | Display | PDB format |
PDBx/mmJSON format | 6l7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/6l7p ftp://data.pdbj.org/pub/pdb/validation_reports/l7/6l7p | HTTPS FTP |
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-Related structure data
Related structure data | 0850MC 0849C 0851C 6l7oC C: citing same article (ref.) M: map data used to model this data |
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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 ... , 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) Strain: BP-1 / References: UniProt: Q8DL61 |
-Sugars , 1 types, 2 molecules
#21: Sugar |
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-Non-polymers , 6 types, 64 molecules
#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 |
-Sample preparation
Component | Name: NDH-1LDelV / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Source (natural) | Organism: Thermosynechococcus elongatus BP-1 (bacteria) |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-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 |