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- EMDB-11237: Respiratory complex I from Thermus thermophilus, NADH dataset, mi... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11237 | |||||||||
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Title | Respiratory complex I from Thermus thermophilus, NADH dataset, minor state | |||||||||
![]() | Postprocessed map, NADH dataset, minor state | |||||||||
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![]() | Respiratory chain / complex I / NADH:ubiquinone oxidoreductase / electron transfer / proton translocation / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() NADH dehydrogenase complex / : / NADH:ubiquinone reductase (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / respiratory chain complex I / molybdopterin cofactor binding / iron-sulfur cluster assembly / NADH dehydrogenase activity / ubiquinone binding ...NADH dehydrogenase complex / : / NADH:ubiquinone reductase (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / respiratory chain complex I / molybdopterin cofactor binding / iron-sulfur cluster assembly / NADH dehydrogenase activity / 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 / ferric iron binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.1 Å | |||||||||
![]() | Kaszuba K / Tambalo M | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 479.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 30.3 KB 30.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.8 KB | Display | ![]() |
Images | ![]() | 55.7 KB | ||
Filedesc metadata | ![]() | 8.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 644.7 KB | Display | ![]() |
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Full document | ![]() | 644.3 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zjnMC ![]() 6i0dC ![]() 6i1pC ![]() 6q8oC ![]() 6q8wC ![]() 6q8xC ![]() 6y11C ![]() 6ziyC ![]() 6zjlC ![]() 6zjyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Postprocessed map, NADH dataset, minor state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.72 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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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: FE2/S2 (INORGANIC) CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6.0 mg/mL |
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Buffer | pH: 6 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III |
Details | with 5 mM NADH |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 - Frames/image: 1-34 / Number grids imaged: 3 / Number real images: 2184 / Average exposure time: 2.0 sec. / Average electron dose: 34.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |