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Open data
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Basic information
Entry | Database: PDB / ID: 7vy1 | ||||||||||||
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Title | Membrane 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 / Mitochondrial protein import / Complex I biogenesis / cellular response to oxygen levels / Respiratory electron transport / Neutrophil degranulation / gliogenesis / Mitochondrial protein degradation ...Mitochondrial Fatty Acid Beta-Oxidation / Glyoxylate metabolism and glycine degradation / protein lipoylation / Mitochondrial protein import / Complex I biogenesis / cellular response to oxygen levels / Respiratory electron transport / Neutrophil degranulation / gliogenesis / Mitochondrial protein degradation / neural precursor cell proliferation / mitochondrial large ribosomal subunit / [2Fe-2S] cluster assembly / oxygen sensor activity / respiratory chain complex I / deoxynucleoside kinase activity / NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone / ubiquinone binding / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / reactive oxygen species metabolic process / electron transport chain / mitochondrial intermembrane space / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / membrane => GO:0016020 / nuclear speck / mitochondrial matrix / ubiquitin protein ligase binding / endoplasmic reticulum / mitochondrion / nucleoplasm / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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 | ![]() | 976.5 KB | Display | ![]() |
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PDB format | ![]() | 792.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 130.9 KB | Display | |
Data in CIF | ![]() | 186.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 32191MC ![]() 7v2cC ![]() 7v2dC ![]() 7v2eC ![]() 7v2fC ![]() 7v2hC ![]() 7v2kC ![]() 7v2rC ![]() 7v30C ![]() 7v31C ![]() 7v32C ![]() 7v33C ![]() 7v3mC ![]() 7vb7C ![]() 7vblC ![]() 7vbnC ![]() 7vbpC ![]() 7vbzC ![]() 7vc0C ![]() 7vwjC ![]() 7vwlC ![]() 7vxpC ![]() 7vxsC ![]() 7vxuC ![]() 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 ... , 18 types, 18 molecules QSUVWYZabcdghnpuvw
#1: Protein | Mass: 53735.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 8088.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 9225.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 14686.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 16911.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 11939.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 11128.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 21587.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 15603.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 21702.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 20944.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 14327.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 12506.591 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#22: Protein | Mass: 7044.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#24: Protein | Mass: 21864.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#27: Protein | Mass: 20064.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#28: Protein | Mass: 16356.690 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#29: Protein | Mass: 40476.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 5 types, 5 molecules Xefjo
#6: Protein | Mass: 17308.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#13: Protein | Mass: 17384.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 8664.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 12798.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: Protein | Mass: 15117.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH-ubiquinone oxidoreductase chain ... , 6 types, 6 molecules iklmrs
#17: Protein | Mass: 39077.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O79875, NADH:ubiquinone reductase (H+-translocating) |
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#19: Protein | Mass: 10827.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P56632, NADH:ubiquinone reductase (H+-translocating) |
#20: Protein | Mass: 68267.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q71K68, NADH:ubiquinone reductase (H+-translocating) |
#21: Protein | Mass: 19021.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O79882, NADH:ubiquinone reductase (H+-translocating) |
#25: Protein | Mass: 51853.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q7IIB7, NADH:ubiquinone reductase (H+-translocating) |
#26: Protein | Mass: 35667.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O79874, NADH:ubiquinone reductase (H+-translocating) |
-Non-polymers , 6 types, 24 molecules ![](data/chem/img/PEE.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/PLX.gif)
![](data/chem/img/UQ.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/PLX.gif)
![](data/chem/img/UQ.gif)
![](data/chem/img/ADP.gif)
#30: Chemical | ChemComp-PEE / #31: Chemical | ChemComp-CDL / #32: Chemical | ChemComp-8Q1 / | #33: Chemical | ChemComp-PLX / ( #34: Chemical | ChemComp-UQ / | #35: Chemical | ChemComp-ADP / | |
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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-#2, #5, #7-#8, #10-#12, #14-#16, #19, #23-#24, #27 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193234 / Symmetry type: POINT |