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Open data
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Basic information
Entry | Database: PDB / ID: 7vxu | ||||||||||||
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Title | Matrix arm of deactive state CI from Q10 dataset | ||||||||||||
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![]() | ELECTRON TRANSPORT / mammalian / mitochondrial / respiratory / complex I | ||||||||||||
Function / homology | ![]() Mitochondrial Fatty Acid Beta-Oxidation / Glyoxylate metabolism and glycine degradation / protein lipoylation / RHOG GTPase cycle / Complex I biogenesis / cellular response to oxygen levels / Respiratory electron transport / gliogenesis / Mitochondrial protein degradation / neural precursor cell proliferation ...Mitochondrial Fatty Acid Beta-Oxidation / Glyoxylate metabolism and glycine degradation / protein lipoylation / RHOG GTPase cycle / Complex I biogenesis / cellular response to oxygen levels / Respiratory electron transport / gliogenesis / Mitochondrial protein degradation / neural precursor cell proliferation / mitochondrial large ribosomal subunit / cardiac muscle tissue development / [2Fe-2S] cluster assembly / oxygen sensor activity / cellular respiration / ubiquinone-6 biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / response to cAMP / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / regulation of protein phosphorylation / mitochondrial intermembrane space / brain development / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / positive regulation of fibroblast proliferation / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / nuclear body / ubiquitin protein ligase binding / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||
![]() | Gu, J.K. / Yang, M.J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The coupling mechanism of mammalian mitochondrial complex I. Authors: Jinke Gu / Tianya Liu / Runyu Guo / Laixing Zhang / Maojun Yang / ![]() Abstract: Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in ...Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in mitochondria. In the present study, we report cryo-electron microscopy structures of CI from Sus scrofa in six treatment conditions at a resolution of 2.4-3.5 Å, in which CI structures of each condition can be classified into two biochemical classes (active or deactive), with a notably higher proportion of active CI particles. These structures illuminate how hydrophobic ubiquinone-10 (Q10) with its long isoprenoid tail is bound and reduced in a narrow Q chamber comprising four different Q10-binding sites. Structural comparisons of active CI structures from our decylubiquinone-NADH and rotenone-NADH datasets reveal that Q10 reduction at site 1 is not coupled to proton pumping in the membrane arm, which might instead be coupled to Q10 oxidation at site 2. Our data overturn the widely accepted previous proposal about the coupling mechanism of CI. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 716.6 KB | Display | ![]() |
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PDB format | ![]() | 572 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 95.8 KB | Display | |
Data in CIF | ![]() | 143.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 32188MC ![]() 7v2cC ![]() 7v2dC ![]() 7v2eC ![]() 7v2fC ![]() 7v2hC ![]() 7v2kC ![]() 7v2rC ![]() 7v30C ![]() 7v31C ![]() 7v32C ![]() 7v33C ![]() 7v3mC ![]() 7vb7C ![]() 7vblC ![]() 7vbnC ![]() 7vbpC ![]() 7vbzC ![]() 7vc0C ![]() 7vwjC ![]() 7vwlC ![]() 7vxpC ![]() 7vxsC ![]() 7vy1C ![]() 7vy8C ![]() 7vy9C ![]() 7vyaC ![]() 7vyeC ![]() 7vyfC ![]() 7vygC ![]() 7vyhC ![]() 7vyiC ![]() 7vynC ![]() 7vysC ![]() 7vz1C ![]() 7vz8C ![]() 7vzvC ![]() 7vzwC ![]() 7w00C ![]() 7w0hC ![]() 7w0rC ![]() 7w0yC ![]() 7w1oC ![]() 7w1pC ![]() 7w1tC ![]() 7w1uC ![]() 7w1vC ![]() 7w1zC ![]() 7w20C ![]() 7w2kC ![]() 7w2lC ![]() 7w2rC ![]() 7w2uC ![]() 7w2yC ![]() 7w31C ![]() 7w32C ![]() 7w35C ![]() 7w4cC ![]() 7w4dC ![]() 7w4eC ![]() 7w4fC ![]() 7w4gC ![]() 7w4jC ![]() 7w4kC ![]() 7w4lC ![]() 7w4mC ![]() 7w4nC ![]() 7w4qC 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
-NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules AKO
#1: Protein | Mass: 50052.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#10: Protein | Mass: 12172.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 27439.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 5 types, 5 molecules BLPQT
#2: Protein | Mass: 23893.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#11: Protein | Mass: 19746.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 30241.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 53735.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 13348.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 4 types, 4 molecules CGJM
#3: Protein | Mass: 21795.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#6: Protein | Mass: 17308.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 42493.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 78670.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 6 types, 6 molecules EFHINW
#4: Protein | Mass: 14953.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#5: Protein | Mass: 11099.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 13321.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 12648.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 17162.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 16911.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 10 types, 16 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/PLX.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/PLX.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/ZN.gif)
#19: Chemical | ChemComp-SF4 / #20: Chemical | ChemComp-FMN / | #21: Chemical | ChemComp-PEE / | #22: Chemical | ChemComp-PLX / ( | #23: Chemical | ChemComp-8Q1 / | #24: Chemical | ChemComp-NDP / | #25: Chemical | #26: Chemical | ChemComp-MG / | #27: Chemical | ChemComp-CDL / | #28: Chemical | ChemComp-ZN / | |
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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 |
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Sample preparation
Component | Name: Respiratory complex I / Type: COMPLEX / Entity ID: #4-#5, #7-#8, #10-#11, #15-#16, #18 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193234 / Symmetry type: POINT |