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Yorodumi- EMDB-14134: Bovine complex I in lipid nanodisc, Deactive-ligand (composite) -
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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | Bovine complex I in lipid nanodisc, Deactive-ligand (composite) | |||||||||
Map data | Composite of 3 globally sharpened focus-refined maps generated using Phenix Combine Focused Maps | |||||||||
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| Function / homology | Function and homology informationComplex I biogenesis / Mitochondrial protein import / RHOG GTPase cycle / ubiquinone biosynthetic process / Respiratory electron transport / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / gliogenesis / Neutrophil degranulation / neural precursor cell proliferation ...Complex I biogenesis / Mitochondrial protein import / RHOG GTPase cycle / ubiquinone biosynthetic process / Respiratory electron transport / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / gliogenesis / Neutrophil degranulation / neural precursor cell proliferation / [2Fe-2S] cluster assembly / oxygen sensor activity / NADH dehydrogenase activity / Mitochondrial protein degradation / ubiquinone binding / acyl binding / electron transport coupled proton transport / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / 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 / circadian rhythm / 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 / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / cytoplasm Similarity search - Function | |||||||||
| Biological species | ![]() ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Chung I / Bridges HR / Hirst J | |||||||||
| Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2022Title: Cryo-EM structures define ubiquinone-10 binding to mitochondrial complex I and conformational transitions accompanying Q-site occupancy. Authors: Injae Chung / John J Wright / Hannah R Bridges / Bozhidar S Ivanov / Olivier Biner / Caroline S Pereira / Guilherme M Arantes / Judy Hirst / ![]() Abstract: Mitochondrial complex I is a central metabolic enzyme that uses the reducing potential of NADH to reduce ubiquinone-10 (Q) and drive four protons across the inner mitochondrial membrane, powering ...Mitochondrial complex I is a central metabolic enzyme that uses the reducing potential of NADH to reduce ubiquinone-10 (Q) and drive four protons across the inner mitochondrial membrane, powering oxidative phosphorylation. Although many complex I structures are now available, the mechanisms of Q reduction and energy transduction remain controversial. Here, we reconstitute mammalian complex I into phospholipid nanodiscs with exogenous Q. Using cryo-EM, we reveal a Q molecule occupying the full length of the Q-binding site in the 'active' (ready-to-go) resting state together with a matching substrate-free structure, and apply molecular dynamics simulations to propose how the charge states of key residues influence the Q binding pose. By comparing ligand-bound and ligand-free forms of the 'deactive' resting state (that require reactivating to catalyse), we begin to define how substrate binding restructures the deactive Q-binding site, providing insights into its physiological and mechanistic relevance. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_14134.map.gz | 929.3 MB | EMDB map data format | |
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| Header (meta data) | emd-14134-v30.xml emd-14134.xml | 68 KB 68 KB | Display Display | EMDB header |
| Images | emd_14134.png | 137.4 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14134 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14134 | HTTPS FTP |
-Validation report
| Summary document | emd_14134_validation.pdf.gz | 546 KB | Display | EMDB validaton report |
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| Full document | emd_14134_full_validation.pdf.gz | 545.6 KB | Display | |
| Data in XML | emd_14134_validation.xml.gz | 9 KB | Display | |
| Data in CIF | emd_14134_validation.cif.gz | 10.4 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14134 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14134 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7qsmMC ![]() 7qskC ![]() 7qslC ![]() 7qsnC ![]() 7qsoC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_14134.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Composite of 3 globally sharpened focus-refined maps generated using Phenix Combine Focused Maps | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.7496 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Mitochondrial complex I in the deactive state with a ligand bound
+Supramolecule #1: Mitochondrial complex I in the deactive state with a ligand bound
+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 75 kDa subunit, mitochondrial
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
+Macromolecule #10: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #14: NADH-ubiquinone oxidoreductase chain 2
+Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...
+Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...
+Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
+Macromolecule #19: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
+Macromolecule #20: Acyl carrier protein, mitochondrial
+Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
+Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
+Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
+Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
+Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #26: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
+Macromolecule #28: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
+Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 subunit C2
+Macromolecule #30: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
+Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
+Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...
+Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...
+Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
+Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mito...
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
+Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
+Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
+Macromolecule #40: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
+Macromolecule #42: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
+Macromolecule #43: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
+Macromolecule #44: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
+Macromolecule #45: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #46: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #47: IRON/SULFUR CLUSTER
+Macromolecule #48: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #49: FLAVIN MONONUCLEOTIDE
+Macromolecule #50: POTASSIUM ION
+Macromolecule #51: GLYCEROL
+Macromolecule #52: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #53: CARDIOLIPIN
+Macromolecule #54: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #55: MAGNESIUM ION
+Macromolecule #56: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #57: ZINC ION
+Macromolecule #58: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
+Macromolecule #59: CHOLIC ACID
+Macromolecule #60: MYRISTIC ACID
+Macromolecule #61: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 4.78 mg/mL | |||||||||
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| Buffer | pH: 7.5 Component:
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| Grid | Model: UltrAuFoil R0.6/1 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE Details: Following glow discharge for 90 s at 20 mA, the grid was treated for 48 hours in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ...Details: Following glow discharge for 90 s at 20 mA, the grid was treated for 48 hours in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ethanol and dried prior to blotting | |||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 10 seconds before plunging. |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 6780 / Average exposure time: 2.4 sec. / Average electron dose: 40.5 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi




Authors
United Kingdom, 1 items
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Processing
FIELD EMISSION GUN
