+
Open data
-
Basic information
Entry | Database: PDB / ID: 6zk9 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Peripheral domain of open complex I during turnover | |||||||||
![]() |
| |||||||||
![]() | ELECTRON TRANSPORT / complex / respiration / NADH / proton pump / mitochondria / iron-sulphur cluster / oxidoreductase / membrane protein | |||||||||
Function / homology | ![]() NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial electron transport, NADH to ubiquinone / : / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity ...NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / apoptotic mitochondrial changes / : / mitochondrial electron transport, NADH to ubiquinone / : / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / ATP metabolic process / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / electron transport chain / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / circadian rhythm / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / mitochondrial matrix / protein-containing complex binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
![]() | Kampjut, D. / Sazanov, L.A. | |||||||||
Funding support | European Union, 2items
| |||||||||
![]() | ![]() Title: The coupling mechanism of mammalian respiratory complex I. Authors: Domen Kampjut / Leonid A Sazanov / ![]() Abstract: Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different ...Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 775.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 619.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 93.8 KB | Display | |
Data in CIF | ![]() | 156.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11241MC ![]() 6zkaC ![]() 6zkbC ![]() 6zkcC ![]() 6zkdC ![]() 6zkeC ![]() 6zkfC ![]() 6zkgC ![]() 6zkhC ![]() 6zkiC ![]() 6zkjC ![]() 6zkkC ![]() 6zklC ![]() 6zkmC ![]() 6zknC ![]() 6zkoC ![]() 6zkpC ![]() 6zkqC ![]() 6zkrC ![]() 6zksC ![]() 6zktC ![]() 6zkuC ![]() 6zkvC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-NADH dehydrogenase [ubiquinone] ... , 4 types, 4 molecules 1cei
#1: Protein | Mass: 50687.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: W5PUX0, NADH dehydrogenase, NADH:ubiquinone reductase (H+-translocating) |
---|---|
#10: Protein | Mass: 19381.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 11097.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Mitochondrial complex I, ... , 9 types, 9 molecules 2469abfhq
#2: Protein | Mass: 27373.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#4: Protein | Mass: 52661.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 24622.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 24496.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 11916.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 13457.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 13287.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 12701.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 16766.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH:ubiquinone oxidoreductase core subunit ... , 2 types, 2 molecules 35
#3: Protein | Mass: 79519.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#5: Protein | Mass: 30384.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH:ubiquinone oxidoreductase subunit ... , 2 types, 2 molecules dg
#11: Protein | Mass: 43025.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#14: Protein | Mass: 16302.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 1 types, 1 molecules j
#17: Protein | Mass: 17608.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Non-polymers , 12 types, 1491 molecules ![](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/PC1.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/ZMP.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/ZMP.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HOH.gif)
#19: Chemical | ChemComp-SF4 / #20: Chemical | ChemComp-FMN / | #21: Chemical | ChemComp-NAI / | #22: Chemical | #23: Chemical | ChemComp-K / | #24: Chemical | #25: Chemical | #26: Chemical | ChemComp-ZN / | #27: Chemical | ChemComp-NDP / | #28: Chemical | ChemComp-ZMP / | #29: Chemical | ChemComp-CDL / | #30: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Peripheral domain of open complex I during turnover / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL |
---|---|
Molecular weight | Value: 1 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-
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 / Cs: 2.7 mm |
Image recording | Electron dose: 100 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 315484 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | B value: 38 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5LNK | ||||||||||||||||||||||||||||
Refine LS restraints |
|