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Yorodumi- PDB-6tjv: Structure of the NDH-1MS complex from Thermosynechococcus elongatus -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tjv | |||||||||||||||
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Title | Structure of the NDH-1MS complex from Thermosynechococcus elongatus | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / carbon concentrating photosynthetic complex I / proton pump | |||||||||||||||
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 / NADH dehydrogenase activity / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport ...: / 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 / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / cell adhesion molecule binding / extracellular matrix / extracellular matrix organization / NADH dehydrogenase (ubiquinone) activity / aerobic respiration / NAD binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / cell adhesion / iron ion binding / extracellular space / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Thermosynechococcus elongatus (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
Authors | Schuller, J.M. / Saura, P. / Thiemann, J. / Schuller, S.K. / Gamiz-Hernandez, A.P. / Kurisu, G. / Nowaczyk, M.M. / Kaila, V.R.I. | |||||||||||||||
Funding support | Germany, 4items
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Citation | Journal: Nat Commun / Year: 2020 Title: Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I. Authors: Jan M Schuller / Patricia Saura / Jacqueline Thiemann / Sandra K Schuller / Ana P Gamiz-Hernandez / Genji Kurisu / Marc M Nowaczyk / Ville R I Kaila / Abstract: Photosynthetic organisms capture light energy to drive their energy metabolism, and employ the chemical reducing power to convert carbon dioxide (CO) into organic molecules. Photorespiration, ...Photosynthetic organisms capture light energy to drive their energy metabolism, and employ the chemical reducing power to convert carbon dioxide (CO) into organic molecules. Photorespiration, however, significantly reduces the photosynthetic yields. To survive under low CO concentrations, cyanobacteria evolved unique carbon-concentration mechanisms that enhance the efficiency of photosynthetic CO fixation, for which the molecular principles have remained unknown. We show here how modular adaptations enabled the cyanobacterial photosynthetic complex I to concentrate CO using a redox-driven proton-pumping machinery. Our cryo-electron microscopy structure at 3.2 Å resolution shows a catalytic carbonic anhydrase module that harbours a Zn active site, with connectivity to proton-pumping subunits that are activated by electron transfer from photosystem I. Our findings illustrate molecular principles in the photosynthetic complex I machinery that enabled cyanobacteria to survive in drastically changing CO conditions. | |||||||||||||||
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 | 6tjv.cif.gz | 750.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tjv.ent.gz | 622.5 KB | Display | PDB format |
PDBx/mmJSON format | 6tjv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tjv_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6tjv_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6tjv_validation.xml.gz | 133.6 KB | Display | |
Data in CIF | 6tjv_validation.cif.gz | 192.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/6tjv ftp://data.pdbj.org/pub/pdb/validation_reports/tj/6tjv | HTTPS FTP |
-Related structure data
Related structure data | 10513MC 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 ABCEHIJKLMNO
#1: Protein | Mass: 40565.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) 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) Thermosynechococcus elongatus (strain BP-1) (bacteria) 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) Thermosynechococcus elongatus (strain BP-1) (bacteria) 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) Thermosynechococcus elongatus (strain BP-1) (bacteria) 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) Thermosynechococcus elongatus (strain BP-1) (bacteria) 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) Thermosynechococcus elongatus (strain BP-1) (bacteria) 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) Thermosynechococcus elongatus (strain BP-1) (bacteria) 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) Thermosynechococcus elongatus (strain BP-1) (bacteria) 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) Thermosynechococcus elongatus (strain BP-1) (bacteria) 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) Thermosynechococcus elongatus (strain BP-1) (bacteria) 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) Thermosynechococcus elongatus (strain BP-1) (bacteria) 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) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: Q8DMU4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
-NADH dehydrogenase subunit ... , 3 types, 3 molecules DFG
#4: Protein | Mass: 53908.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: Q8DKF4 |
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#6: Protein | Mass: 66283.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: Q8DKF5 |
#7: Protein | Mass: 21580.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: Q8DL30, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
-Protein , 3 types, 3 molecules PQS
#16: Protein | Mass: 51003.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: Q8DKF3 |
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#17: Protein | Mass: 15785.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: Q8DMA1 |
#18: Protein | Mass: 12462.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) References: UniProt: Q8DL61 |
-Sugars , 1 types, 2 molecules
#19: Sugar |
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-Non-polymers , 7 types, 14 molecules
#20: Chemical | #21: Chemical | ChemComp-SQD / #22: Chemical | ChemComp-BCR / | #23: Chemical | ChemComp-CLA / | #24: Chemical | #25: Chemical | ChemComp-ZN / | #26: Water | ChemComp-HOH / | |
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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 |
-Sample preparation
Component | Name: NDH-1MS / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Thermosynechococcus elongatus BP-1 (bacteria) |
Buffer solution | pH: 7.5 |
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: 40.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170151 / Symmetry type: POINT | ||||||||||||||||||||||||
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