+
Open data
-
Basic information
| Entry | Database: EMDB / ID: EMD-3731 | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Title | Mitochondrial complex I in the deactive state | |||||||||
Map data | Bovine mitochondrial complex I in the deactive state | |||||||||
Sample |
| |||||||||
Keywords | Complex I / redox enzyme / proton pump / membrane protein / oxidoreductase | |||||||||
| Function / homology | Function and homology informationComplex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / [2Fe-2S] cluster assembly / oxygen sensor activity / Neutrophil degranulation ...Complex I biogenesis / RHOG GTPase cycle / Respiratory electron transport / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / [2Fe-2S] cluster assembly / oxygen sensor activity / Neutrophil degranulation / NADH dehydrogenase activity / Mitochondrial protein degradation / acyl binding / ubiquinone binding / electron transport coupled proton transport / acyl carrier activity / mitochondrial ATP synthesis coupled electron transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / response to cAMP / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / neurogenesis / reactive oxygen species metabolic process / aerobic respiration / fatty acid binding / respiratory electron transport chain / electron transport chain / brain development / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / fatty acid biosynthetic process / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / mitochondrial matrix / negative regulation of DNA-templated transcription / apoptotic process / mitochondrion / nucleoplasm / metal ion binding / cytoplasm Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 4.13 Å | |||||||||
Authors | Blaza JN / Vinothkumar KR | |||||||||
| Funding support | United Kingdom, 2 items
| |||||||||
Citation | Journal: Structure / Year: 2018Title: Structure of the Deactive State of Mammalian Respiratory Complex I. Authors: James N Blaza / Kutti R Vinothkumar / Judy Hirst / ![]() Abstract: Complex I (NADH:ubiquinone oxidoreductase) is central to energy metabolism in mammalian mitochondria. It couples NADH oxidation by ubiquinone to proton transport across the energy-conserving inner ...Complex I (NADH:ubiquinone oxidoreductase) is central to energy metabolism in mammalian mitochondria. It couples NADH oxidation by ubiquinone to proton transport across the energy-conserving inner membrane, catalyzing respiration and driving ATP synthesis. In the absence of substrates, active complex I gradually enters a pronounced resting or deactive state. The active-deactive transition occurs during ischemia and is crucial for controlling how respiration recovers upon reperfusion. Here, we set a highly active preparation of Bos taurus complex I into the biochemically defined deactive state, and used single-particle electron cryomicroscopy to determine its structure to 4.1 Å resolution. We show that the deactive state arises when critical structural elements that form the ubiquinone-binding site become disordered, and we propose reactivation is induced when substrate binding to the NADH-reduced enzyme templates their reordering. Our structure both rationalizes biochemical data on the deactive state and offers new insights into its physiological and cellular roles. | |||||||||
| History |
|
-
Structure visualization
| Movie |
Movie viewer |
|---|---|
| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
| Supplemental images |
-
Downloads & links
-EMDB archive
| Map data | emd_3731.map.gz | 166.9 MB | EMDB map data format | |
|---|---|---|---|---|
| Header (meta data) | emd-3731-v30.xml emd-3731.xml | 64.9 KB 64.9 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_3731_fsc.xml | 12.6 KB | Display | FSC data file |
| Images | emd_3731.png | 67.8 KB | ||
| Filedesc metadata | emd-3731.cif.gz | 12.8 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3731 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3731 | HTTPS FTP |
-Validation report
| Summary document | emd_3731_validation.pdf.gz | 643.6 KB | Display | EMDB validaton report |
|---|---|---|---|---|
| Full document | emd_3731_full_validation.pdf.gz | 643.1 KB | Display | |
| Data in XML | emd_3731_validation.xml.gz | 12.3 KB | Display | |
| Data in CIF | emd_3731_validation.cif.gz | 16.9 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3731 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3731 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 5o31MC ![]() 3733C M: atomic model generated by this map C: citing same article ( |
|---|---|
| Similar structure data |
-
Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
|---|---|
| Related items in Molecule of the Month |
-
Map
| File | Download / File: emd_3731.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Bovine mitochondrial complex I in the deactive state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
CCP4 map header:
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Supplemental data
-
Sample components
+Entire : Mitochondrial complex I in the deactive state
+Supramolecule #1: Mitochondrial complex I in the deactive state
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
+Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
+Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
+Macromolecule #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
+Macromolecule #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #7: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #8: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #9: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #10: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #14: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #17: Acyl carrier protein, mitochondrial
+Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #20: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH...
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #24: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH ...
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH...
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #34: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
+Macromolecule #35: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #36: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #37: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [...
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #44: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NAD...
+Macromolecule #45: IRON/SULFUR CLUSTER
+Macromolecule #46: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #47: FLAVIN MONONUCLEOTIDE
+Macromolecule #48: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #49: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
|---|---|
Processing | single particle reconstruction |
| Aggregation state | particle |
-
Sample preparation
| Concentration | 4 mg/mL | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Buffer | pH: 7.55 Component:
| ||||||||||||
| Grid | Model: Quantifoil UltrAuFoil R0.6/1 / Material: GOLD / Details: The grid was PEGylated before use | ||||||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
| Details | Monodisperse bovine mitochondrial complex I isolated in the detergent cymal-7 |
-
Electron microscopy
| Microscope | FEI TITAN KRIOS |
|---|---|
| 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: 1-20 / Number grids imaged: 1 / Number real images: 2954 / Average exposure time: 2.5 sec. / Average electron dose: 80.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 101499 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 59000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
| Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 78.7 |
|---|---|
| Output model | ![]() PDB-5o31: |
Movie
Controller
About Yorodumi



Keywords
Authors
United Kingdom, 2 items
Citation
UCSF Chimera



































Z (Sec.)
Y (Row.)
X (Col.)




























