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Open data
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Basic information
Entry | Database: PDB / ID: 7vy8 | ||||||||||||
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Title | Matrix arm of active state CI from Q10-NADH dataset | ||||||||||||
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![]() | ELECTRON TRANSPORT / mammalian / mitochondrial / respiratory / complex I | ||||||||||||
Function / homology | ![]() RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Mitochondrial protein degradation / cardiac muscle tissue development / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport ...RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Mitochondrial protein degradation / cardiac muscle tissue development / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / acyl binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / electron transport chain / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / nuclear body / protein-containing complex binding / mitochondrion / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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 | ![]() | 718.4 KB | Display | ![]() |
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PDB format | ![]() | 577.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 96.7 KB | Display | |
Data in CIF | ![]() | 145 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 32196MC ![]() 7v2cC ![]() 7v2dC ![]() 7v2eC ![]() 7v2fC ![]() 7v2hC ![]() 7v2kC ![]() 7v2rC ![]() 7v30C ![]() 7v31C ![]() 7v32C ![]() 7v33C ![]() 7v3mC ![]() 7vb7C ![]() 7vblC ![]() 7vbnC ![]() 7vbpC ![]() 7vbzC ![]() 7vc0C ![]() 7vwjC ![]() 7vwlC ![]() 7vxpC ![]() 7vxsC ![]() 7vxuC ![]() 7vy1C ![]() 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 ... , 2 types, 2 molecules AO
#1: Protein | Mass: 47434.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: F1RVN1, NADH:ubiquinone reductase (H+-translocating) |
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#14: Protein | Mass: 23826.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 5 types, 5 molecules BCLQT
#2: Protein | Mass: 20207.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Protein | Mass: 17874.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 14442.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 44127.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 10567.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 5 types, 5 molecules EFINW
#4: Protein | Mass: 13812.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#5: Protein | Mass: 9841.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 12517.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 17031.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein/peptide | Mass: 3204.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 2 molecules GJ
#6: Protein | Mass: 10133.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#9: Protein | Mass: 38954.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH-ubiquinone oxidoreductase ... , 4 types, 4 molecules HKMP
#7: Protein | Mass: 12949.106 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#10: Protein/peptide | Mass: 5193.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 75770.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 24521.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 12 types, 18 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/PLX.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/UQ.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/PEE.gif)
![](data/chem/img/PLX.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/UQ.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
#19: Chemical | ChemComp-SF4 / #20: Chemical | ChemComp-FMN / | #21: Chemical | ChemComp-NAI / | #22: Chemical | ChemComp-PEE / | #23: Chemical | ChemComp-PLX / ( | #24: Chemical | ChemComp-8Q1 / | #25: Chemical | ChemComp-CDL / | #26: Chemical | ChemComp-NDP / | #27: Chemical | ChemComp-UQ / | #28: Chemical | #29: Chemical | ChemComp-MG / | #30: 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: #1-#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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152604 / Symmetry type: POINT |