[English] 日本語
![](img/lk-miru.gif)
- EMDB-11235: Respiratory complex I from Thermus thermophilus, NAD+ dataset, ma... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-11235 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Respiratory complex I from Thermus thermophilus, NAD+ dataset, major state![]() | |||||||||
![]() | Postprocessed map, NAD dataset, major state | |||||||||
![]() |
| |||||||||
Function / homology | ![]() plasma membrane respiratory chain complex I / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kaszuba K / Tambalo M / Gallagher GT / Sazanov LA | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Key role of quinone in the mechanism of respiratory complex I. Authors: Javier Gutiérrez-Fernández / Karol Kaszuba / Gurdeep S Minhas / Rozbeh Baradaran / Margherita Tambalo / David T Gallagher / Leonid A Sazanov / ![]() ![]() ![]() Abstract: Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in ...Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 479.6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 29.7 KB 29.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18 KB | Display | ![]() |
Images | ![]() | 212.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zjlMC ![]() 6i0dC ![]() 6i1pC ![]() 6q8oC ![]() 6q8wC ![]() 6q8xC ![]() 6y11C ![]() 6ziyC ![]() 6zjnC ![]() 6zjyC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Postprocessed map, NAD dataset, major state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.72 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : Respiratory complex I from Thermus thermophilus
+Supramolecule #1: Respiratory complex I from Thermus thermophilus
+Macromolecule #1: NADH-quinone oxidoreductase subunit 1
+Macromolecule #2: NADH-quinone oxidoreductase subunit 2
+Macromolecule #3: NADH-quinone oxidoreductase subunit 3
+Macromolecule #4: NADH-quinone oxidoreductase subunit 4
+Macromolecule #5: NADH-quinone oxidoreductase subunit 5
+Macromolecule #6: NADH-quinone oxidoreductase subunit 6
+Macromolecule #7: NADH-quinone oxidoreductase subunit 9
+Macromolecule #8: NADH-quinone oxidoreductase subunit 15
+Macromolecule #9: NADH-quinone oxidoreductase subunit 7
+Macromolecule #10: NADH-quinone oxidoreductase subunit 10
+Macromolecule #11: NADH-quinone oxidoreductase subunit 11
+Macromolecule #12: NADH-quinone oxidoreductase subunit 12
+Macromolecule #13: NADH-quinone oxidoreductase subunit 13
+Macromolecule #14: NADH-quinone oxidoreductase subunit 14
+Macromolecule #15: NADH-quinone oxidoreductase subunit 8
+Macromolecule #16: IRON/SULFUR CLUSTER
+Macromolecule #17: FLAVIN MONONUCLEOTIDE
+Macromolecule #18: FE2/S2 (INORGANIC) CLUSTER
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Concentration | 6.0 mg/mL |
---|---|
Buffer | pH: 6 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III |
Details | with 5 mM NAD+ |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-34 / Number grids imaged: 1 / Number real images: 710 / Average exposure time: 2.0 sec. / Average electron dose: 34.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |