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Yorodumi- PDB-6hum: Structure of the photosynthetic complex I from Thermosynechococcu... -
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-Basic information
Entry | Database: PDB / ID: 6hum | ||||||||||||||||||||||||
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Title | Structure of the photosynthetic complex I from Thermosynechococcus elongatus | ||||||||||||||||||||||||
Components |
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Keywords | PROTON TRANSPORT / Respiratory Complex / Ferredoxin / Cyclic electron flow / Complex I / Membrane protein complex | ||||||||||||||||||||||||
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 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 / plasma membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | Thermosynechococcus elongatus BP-1 (bacteria) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å | ||||||||||||||||||||||||
Authors | Schuller, J.M. / Schuller, S.K. / Kurisu, G. / Engel, B.D. / Nowaczyk, M.M. | ||||||||||||||||||||||||
Funding support | Germany, Japan, Australia, 7items
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Citation | Journal: Science / Year: 2019 Title: Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer. Authors: Jan M Schuller / James A Birrell / Hideaki Tanaka / Tsuyoshi Konuma / Hannes Wulfhorst / Nicholas Cox / Sandra K Schuller / Jacqueline Thiemann / Wolfgang Lubitz / Pierre Sétif / Takahisa ...Authors: Jan M Schuller / James A Birrell / Hideaki Tanaka / Tsuyoshi Konuma / Hannes Wulfhorst / Nicholas Cox / Sandra K Schuller / Jacqueline Thiemann / Wolfgang Lubitz / Pierre Sétif / Takahisa Ikegami / Benjamin D Engel / Genji Kurisu / Marc M Nowaczyk / Abstract: Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-angstrom-resolution cryo-electron microscopy ...Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-angstrom-resolution cryo-electron microscopy structure of photosynthetic complex I from the cyanobacterium The model reveals structural adaptations that facilitate binding and electron transfer from the photosynthetic electron carrier ferredoxin. By mimicking cyclic electron flow with isolated components in vitro, we demonstrate that ferredoxin directly mediates electron transfer between photosystem I and complex I, instead of using intermediates such as NADPH (the reduced form of nicotinamide adenine dinucleotide phosphate). A large rate constant for association of ferredoxin to complex I indicates efficient recognition, with the protein subunit NdhS being the key component in this process. | ||||||||||||||||||||||||
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 | 6hum.cif.gz | 761.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hum.ent.gz | 601.1 KB | Display | PDB format |
PDBx/mmJSON format | 6hum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hum_validation.pdf.gz | 911.6 KB | Display | wwPDB validaton report |
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Full document | 6hum_full_validation.pdf.gz | 956.8 KB | Display | |
Data in XML | 6hum_validation.xml.gz | 99 KB | Display | |
Data in CIF | 6hum_validation.cif.gz | 153.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/6hum ftp://data.pdbj.org/pub/pdb/validation_reports/hu/6hum | HTTPS FTP |
-Related structure data
Related structure data | 0281MC 6a7kC M: map data used to model this data C: citing same article (ref.) |
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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 ... , 12 types, 12 molecules ACEBJHIKLNMO
#1: Protein | Mass: 40565.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DL32, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
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#2: Protein | Mass: 15013.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DJ02, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#4: Protein | Mass: 11140.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DL29, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#5: Protein | Mass: 55168.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DMR6, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#7: Protein | Mass: 19363.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DJ01, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#9: Protein | Mass: 45271.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DJD9, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#10: Protein | Mass: 22444.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DL31, 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) Thermosynechococcus elongatus BP-1 (bacteria) 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) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DKZ3, 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) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DJU2, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#15: Protein | Mass: 12584.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DLN5, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
#17: Protein | Mass: 7877.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DMU4, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
-Protein , 2 types, 2 molecules DS
#3: Protein | Mass: 57847.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DKY0, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
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#16: Protein | Mass: 12462.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DL61 |
-NADH dehydrogenase subunit ... , 2 types, 2 molecules GF
#6: Protein | Mass: 21580.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DL30 |
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#13: Protein | Mass: 72025.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) References: UniProt: Q8DKX9 |
-Proton-translocating NADH-quinone dehydrogenase subunit ... , 2 types, 2 molecules PQ
#8: Protein/peptide | Mass: 4630.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) |
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#18: Protein/peptide | Mass: 4206.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria) |
-Non-polymers , 3 types, 5 molecules
#19: Chemical | ChemComp-BCR / |
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#20: Chemical | ChemComp-LMG / |
#21: Chemical |
-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: photosynthetic complex I / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Source (natural) | Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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 FIELD |
Image recording | Electron dose: 49.93 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133485 / Symmetry type: POINT |