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Open data
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Basic information
Entry | Database: PDB / ID: 7zdp | ||||||
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Title | Complex I from Ovis aries at pH9, Open state | ||||||
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![]() | PROTON TRANSPORT / Complex I / respiration / NADH / proton pump / mitochondria / iron-sulphur cluster / oxidoreductase / membrane protein / Quinone | ||||||
Function / homology | ![]() myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / positive regulation of macrophage chemotaxis / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / ubiquinone binding / acyl carrier activity ...myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / positive regulation of macrophage chemotaxis / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / ubiquinone binding / acyl carrier activity / positive regulation of myoblast differentiation / quinone binding / electron transport coupled proton transport / : / positive regulation of lamellipodium assembly / ATP synthesis coupled electron transport / ATP metabolic process / mitochondrial ATP synthesis coupled electron transport / transcription coregulator activity / mitochondrial respiratory chain complex I assembly / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / circadian rhythm / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / membrane => GO:0016020 / mitochondrial inner membrane / mitochondrial matrix / chromatin / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å | ||||||
![]() | Sazanov, L. / Petrova, O. | ||||||
Funding support | European Union, 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 14664MC ![]() 7p61C ![]() 7p62C ![]() 7p63C ![]() 7p64C ![]() 7p69C ![]() 7p7cC ![]() 7p7eC ![]() 7p7jC ![]() 7p7kC ![]() 7p7lC ![]() 7p7mC ![]() 7z7rC ![]() 7z7sC ![]() 7z7tC ![]() 7z7vC ![]() 7z80C ![]() 7z83C ![]() 7z84C ![]() 7zc5C ![]() 7zciC ![]() 7zd6C ![]() 7zdhC ![]() 7zdjC ![]() 7zdmC ![]() 7zebC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 18 types, 19 molecules 4VWXjZmnstuwz3569fg
#1: Protein | Mass: 52661.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||||||||||||||||||||||
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#9: Protein | Mass: 14652.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||||||||||||||||||||||
#10: Protein | Mass: 16317.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||||||||||||||||||||||
#11: Protein | Mass: 17608.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | | Mass: 20526.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | | Mass: 8869.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | | Mass: 8958.202 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #22: Protein | | Mass: 14963.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #23: Protein | | Mass: 21517.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #24: Protein | | Mass: 7898.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #26: Protein | | Mass: 11998.386 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #29: Protein | | Mass: 8211.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #32: Protein | | Mass: 75520.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #33: Protein | | Mass: 24381.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #34: Protein | | Mass: 17860.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #35: Protein | | Mass: 20219.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #41: Protein | | Mass: 13028.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #42: Protein | | Mass: 13767.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules AHJKLMN
#2: Protein | Mass: 13106.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78753, NADH:ubiquinone reductase (H+-translocating) |
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#3: Protein | Mass: 35884.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78747, NADH:ubiquinone reductase (H+-translocating) |
#4: Protein | Mass: 19126.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78757, NADH:ubiquinone reductase (H+-translocating) |
#5: Protein | Mass: 10868.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78754, NADH:ubiquinone reductase (H+-translocating) |
#6: Protein | Mass: 68438.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78756, NADH:ubiquinone reductase (H+-translocating) |
#7: Protein | Mass: 52086.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78755, NADH:ubiquinone reductase (H+-translocating) |
#8: Protein | Mass: 39149.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O78748, NADH:ubiquinone reductase (H+-translocating) |
-NADH dehydrogenase [ubiquinone] 1 ... , 7 types, 7 molecules Ykoqvei
#12: Protein | Mass: 20008.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#14: Protein | Mass: 36883.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 14231.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#20: Protein | Mass: 16766.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#25: Protein | Mass: 18521.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#40: Protein | Mass: 9841.279 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#44: Protein | Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 3 types, 3 molecules lbc
#15: Protein | Mass: 12474.397 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#37: Protein | Mass: 10513.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#38: Protein | Mass: 14559.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH:ubiquinone oxidoreductase subunit ... , 2 types, 2 molecules pd
#19: Protein | Mass: 14975.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#39: Protein | Mass: 43025.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Mitochondrial complex I, ... , 2 types, 2 molecules rh
#21: Protein | Mass: 15565.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#43: Protein | Mass: 12701.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein/peptide , 3 types, 3 molecules xya
#27: Protein/peptide | Mass: 5808.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#28: Protein/peptide | Mass: 6146.106 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#36: Protein/peptide | Mass: 5263.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules 12
#30: Protein | Mass: 47186.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A835ZPN7, NADH:ubiquinone reductase (H+-translocating) |
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#31: Protein | Mass: 23598.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 10 types, 17 molecules ![](data/chem/img/ZMP.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NDP.gif)
#45: Chemical | #46: Chemical | ChemComp-AMP / | #47: Chemical | ChemComp-MYR / | #48: Chemical | ChemComp-SF4 / #49: Chemical | ChemComp-FMN / | #50: Chemical | ChemComp-NAI / | #51: Chemical | #52: Chemical | ChemComp-K / | #53: Chemical | ChemComp-ZN / | #54: Chemical | ChemComp-NDP / | |
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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 |
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Sample preparation
Component | Name: Complex I from Ovis aries at pH9, Open state / Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL |
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Molecular weight | Value: 1 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 9 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R0.6/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 3.3 sec. / Electron dose: 90 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: dev_4092: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35957 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation coefficient | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 6ZKE | ||||||||||||||||||||||||
Refine LS restraints |
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