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Yorodumi- PDB-7z80: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z80 | ||||||
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Title | Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Closed state | ||||||
Components |
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Keywords | PROTON TRANSPORT / Complex I / NADH / Quinone | ||||||
Function / homology | Function and homology information : / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / NADH dehydrogenase activity / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity ...: / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / NADH dehydrogenase activity / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / aerobic respiration / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli BL21 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å | ||||||
Authors | Kravchuk, V. / Kampjut, D. / Sazanov, L. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Nature / Year: 2022 Title: A universal coupling mechanism of respiratory complex I. Authors: Vladyslav Kravchuk / Olga Petrova / Domen Kampjut / Anna Wojciechowska-Bason / Zara Breese / Leonid Sazanov / Abstract: Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone ...Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a 'domino effect' series of proton transfers and electrostatic interactions: the forward wave ('dominoes stacking') primes the pump, and the reverse wave ('dominoes falling') results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z80.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7z80.ent.gz | 767.9 KB | Display | PDB format |
PDBx/mmJSON format | 7z80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z80_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7z80_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7z80_validation.xml.gz | 123.5 KB | Display | |
Data in CIF | 7z80_validation.cif.gz | 193 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/7z80 ftp://data.pdbj.org/pub/pdb/validation_reports/z8/7z80 | HTTPS FTP |
-Related structure data
Related structure data | 14540MC 7p61C 7p62C 7p63C 7p64C 7p69C 7p7cC 7p7eC 7p7jC 7p7kC 7p7lC 7p7mC 7z7rC 7z7sC 7z7tC 7z7vC 7z83C 7z84C 7zc5C 7zciC 7zd6C 7zdhC 7zdjC 7zdmC 7zdpC 7zebC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-NADH-quinone oxidoreductase subunit ... , 10 types, 10 molecules FCBIHALNKJ
#1: Protein | Mass: 49352.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A037YNA7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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#4: Protein | Mass: 68810.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A839KEA0 |
#5: Protein | Mass: 25081.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) References: UniProt: E7T2M5, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#6: Protein | Mass: 20562.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A4V1DR98, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#7: Protein | Mass: 36240.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) References: UniProt: E6BKM7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#8: Protein | Mass: 16474.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A358FP87, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#9: Protein | Mass: 66513.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A1V3W1N5, NADH dehydrogenase (quinone) |
#11: Protein | Mass: 52072.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) References: UniProt: E2QPD7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#12: Protein | Mass: 10852.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A7U9LRT0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
#13: Protein | Mass: 19889.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0H3MIP2, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
-NADH dehydrogenase I subunit ... , 2 types, 2 molecules EM
#2: Protein | Mass: 18614.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A829CRH1 |
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#10: Protein | Mass: 56560.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3T2G7 |
-Protein , 1 types, 1 molecules G
#3: Protein | Mass: 100349.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A8A5GYF0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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-Non-polymers , 8 types, 28 molecules
#14: Chemical | ChemComp-SF4 / #15: Chemical | ChemComp-FMN / | #16: Chemical | ChemComp-NAI / | #17: Chemical | #18: Chemical | ChemComp-CA / | #19: Chemical | ChemComp-3PE / #20: Chemical | #21: Chemical | ChemComp-LFA / |
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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: Complex I / Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL | |||||||||||||||||||||||||||||||||||||||||||||
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) | |||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid type: Quantifoil R0.6/1 | |||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 K |
-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 / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8659 |
Image scans | Sampling size: 5 µm |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1648181 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32655 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: ML | ||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.17 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints |
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