+
Open data
-
Basic information
Entry | Database: PDB / ID: 7vys | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Membrane arm of active state CI from Q1-NADH dataset | ||||||||||||
![]() |
| ||||||||||||
![]() | ELECTRON TRANSPORT / mammalian / mitochondrial / respiratory / complex I | ||||||||||||
Function / homology | ![]() Mitochondrial protein import / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / Mitochondrial protein degradation / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone ...Mitochondrial protein import / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / Mitochondrial protein degradation / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / ubiquinone binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier 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 / NAD binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / nuclear speck / mitochondrial matrix / endoplasmic reticulum / mitochondrion / nucleoplasm / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||||||||
![]() | Gu, J.K. / Yang, M.J. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 991.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 807.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 32214MC ![]() 7v2cC ![]() 7v2dC ![]() 7v2eC ![]() 7v2fC ![]() 7v2hC ![]() 7v2kC ![]() 7v2rC ![]() 7v30C ![]() 7v31C ![]() 7v32C ![]() 7v33C ![]() 7v3mC ![]() 7vb7C ![]() 7vblC ![]() 7vbnC ![]() 7vbpC ![]() 7vbzC ![]() 7vc0C ![]() 7vwjC ![]() 7vwlC ![]() 7vxpC ![]() 7vxsC ![]() 7vxuC ![]() 7vy1C ![]() 7vy8C ![]() 7vy9C ![]() 7vyaC ![]() 7vyeC ![]() 7vyfC ![]() 7vygC ![]() 7vyhC ![]() 7vyiC ![]() 7vynC ![]() 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 ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 2 types, 2 molecules Qh
#1: Protein/peptide | Mass: 5124.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#16: Protein | Mass: 12375.395 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 SUVWuw
#2: Protein | Mass: 8088.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#3: Protein | Mass: 9094.372 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 14555.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 13522.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#27: Protein | Mass: 19932.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#29: Protein | Mass: 36792.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 1 types, 1 molecules X
#6: Protein | Mass: 10133.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules YZabcdenopv
#7: Protein | Mass: 8201.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#8: Protein | Mass: 9042.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 16281.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 15333.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 18608.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 20813.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 12311.712 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#22: Protein | Mass: 6781.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: Protein | Mass: 14986.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#24: Protein | Mass: 21733.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#28: Protein | Mass: 15176.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules fg
#14: Protein/peptide | Mass: 5881.825 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) ![]() ![]() |
-NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules ijklmrs
#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) |
---|---|
#18: Protein | Mass: 12998.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O79880, NADH:ubiquinone reductase (H+-translocating) |
#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: 68697.469 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: 51690.184 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 , 8 types, 453 molecules ![](data/chem/img/PEE.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/PLX.gif)
![](data/chem/img/TYR.gif)
![](data/chem/img/UQ.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/PLX.gif)
![](data/chem/img/TYR.gif)
![](data/chem/img/UQ.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
#30: Chemical | ChemComp-PEE / #31: Chemical | ChemComp-CDL / #32: Chemical | ChemComp-8Q1 / | #33: Chemical | ChemComp-PLX / ( #34: Chemical | ChemComp-TYR / | #35: Chemical | ChemComp-UQ / | #36: Chemical | ChemComp-ADP / | #37: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Respiratory complex I / Type: COMPLEX / Entity ID: #1-#2, #5, #7-#8, #10-#12, #14-#16, #23-#24, #27 / Source: NATURAL |
---|---|
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 |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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) |
-
Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 302353 / Symmetry type: POINT |