[English] 日本語
![](img/lk-miru.gif)
- EMDB-15083: Peripheral arm of Complex I from Ovis aries at pH5.5, Closed state -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Peripheral arm of Complex I from Ovis aries at pH5.5, Closed state | |||||||||
![]() | Peripheral arm postprocessed focus refined map | |||||||||
![]() |
| |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Sazanov L / Petrova O | |||||||||
Funding support | 1 items
| |||||||||
![]() | ![]() Title: A universal coupling mechanism of respiratory complex I. Authors: Vladyslav Kravchuk / Olga Petrova / Domen Kampjut / Anna Wojciechowska-Bason / Zara Breese / Leonid Sazanov / ![]() ![]() ![]() Abstract: Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone ...Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a 'domino effect' series of proton transfers and electrostatic interactions: the forward wave ('dominoes stacking') primes the pump, and the reverse wave ('dominoes falling') results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 25.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 21.5 KB 21.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.8 KB | Display | ![]() |
Images | ![]() | 120.3 KB | ||
Others | ![]() ![]() ![]() | 391.1 MB 393.7 MB 392.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p61C ![]() 7p62C ![]() 7p63C ![]() 7p64C ![]() 7p69C ![]() 7p7cC ![]() 7p7eC ![]() 7p7jC ![]() 7p7kC ![]() 7p7lC ![]() 7p7mC ![]() 7z7rC ![]() 7z7sC ![]() 7z7tC ![]() 7z7vC ![]() 7z80C ![]() 7z83C ![]() 7z84C ![]() 7zc5C ![]() 7zciC ![]() 7zd6C ![]() 7zdhC ![]() 7zdjC ![]() 7zdmC ![]() 7zdpC ![]() 7zebC C: citing same article ( |
---|
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Peripheral arm postprocessed focus refined map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.22 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: Peripheral arm focus refined map
File | emd_15083_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Peripheral arm focus refined map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_15083_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_15083_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Complex I from Ovis aries at pH5.5, Closed state
Entire | Name: Complex I from Ovis aries at pH5.5, Closed state |
---|---|
Components |
|
-Supramolecule #1: Complex I from Ovis aries at pH5.5, Closed state
Supramolecule | Name: Complex I from Ovis aries at pH5.5, Closed state / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#44 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 1 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 3 mg/mL |
---|---|
Buffer | pH: 5.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | TFS GLACIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average exposure time: 3.3 sec. / Average electron dose: 90.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000 |
Sample stage | Cooling holder cryogen: NITROGEN |
+
Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
---|---|
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: correlation coefficient |