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Yorodumi- EMDB-18057: Outward-facing, open2 proteoliposome complex I at 3.1 A. Initiall... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18057 | |||||||||
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Title | Outward-facing, open2 proteoliposome complex I at 3.1 A. Initially purified in DDM. | |||||||||
Map data | Postprocessed consensus map at the calibrated pixel size of 1.35 | |||||||||
Sample |
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Keywords | Complex I / Oxidoreductase / Proteoliposomes / Membrane-bound / metabolism / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Complex I biogenesis / Mitochondrial protein import / RHOG GTPase cycle / ubiquinone-6 biosynthetic process / Respiratory electron transport / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / gliogenesis / neural precursor cell proliferation / [2Fe-2S] cluster assembly ...Complex I biogenesis / Mitochondrial protein import / RHOG GTPase cycle / ubiquinone-6 biosynthetic process / 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 / cellular respiration / Neutrophil degranulation / ubiquinone binding / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / respiratory chain complex I / : / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / ATP metabolic process / response to cAMP / aerobic respiration / neurogenesis / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / fatty acid binding / mitochondrial membrane / electron transport chain / brain development / regulation of protein phosphorylation / mitochondrial intermembrane space / fatty acid biosynthetic process / 2 iron, 2 sulfur cluster binding / positive regulation of fibroblast proliferation / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / protein-containing complex binding / apoptotic process / mitochondrion / nucleoplasm / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Grba DN / Hirst J | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Science / Year: 2024 Title: Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I. Authors: Daniel N Grba / John J Wright / Zhan Yin / William Fisher / Judy Hirst / Abstract: Respiratory complex I is an efficient driver for oxidative phosphorylation in mammalian mitochondria, but its uncontrolled catalysis under challenging conditions leads to oxidative stress and ...Respiratory complex I is an efficient driver for oxidative phosphorylation in mammalian mitochondria, but its uncontrolled catalysis under challenging conditions leads to oxidative stress and cellular damage. Ischemic conditions switch complex I from rapid, reversible catalysis into a dormant state that protects upon reoxygenation, but the molecular basis for the switch is unknown. We combined precise biochemical definition of complex I catalysis with high-resolution cryo-electron microscopy structures in the phospholipid bilayer of coupled vesicles to reveal the mechanism of the transition into the dormant state, modulated by membrane interactions. By implementing a versatile membrane system to unite structure and function, attributing catalytic and regulatory properties to specific structural states, we define how a conformational switch in complex I controls its physiological roles. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18057.map.gz | 11.3 MB | EMDB map data format | |
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Header (meta data) | emd-18057-v30.xml emd-18057.xml | 71.7 KB 71.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18057_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_18057.png | 95.3 KB | ||
Masks | emd_18057_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-18057.cif.gz | 15 KB | ||
Others | emd_18057_additional_1.map.gz emd_18057_half_map_1.map.gz emd_18057_half_map_2.map.gz | 165 MB 165.6 MB 165.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18057 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18057 | HTTPS FTP |
-Validation report
Summary document | emd_18057_validation.pdf.gz | 840.7 KB | Display | EMDB validaton report |
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Full document | emd_18057_full_validation.pdf.gz | 840.3 KB | Display | |
Data in XML | emd_18057_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | emd_18057_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18057 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18057 | HTTPS FTP |
-Related structure data
Related structure data | 8q0oMC 8q0aC 8q0fC 8q0jC 8q0mC 8q0qC 8q1pC 8q1uC 8q1yC 8q25C 8q45C 8q46C 8q47C 8q48C 8q49C 8q4aC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18057.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed consensus map at the calibrated pixel size of 1.35 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18057_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unfiltered consensus map at nominal pixel size of 1.43
File | emd_18057_additional_1.map | ||||||||||||
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Annotation | Unfiltered consensus map at nominal pixel size of 1.43 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Postprocessed consensus map at the calibrated pixel size of 1.35
File | emd_18057_half_map_1.map | ||||||||||||
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Annotation | Postprocessed consensus map at the calibrated pixel size of 1.35 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Postprocessed consensus map at the calibrated pixel size of 1.35
File | emd_18057_half_map_2.map | ||||||||||||
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Annotation | Postprocessed consensus map at the calibrated pixel size of 1.35 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex I from Bos taurus reconstituted into proteoliposomes.
+Supramolecule #1: Complex I from Bos taurus reconstituted into proteoliposomes.
+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: DIUNDECYL PHOSPHATIDYL CHOLINE
+Macromolecule #49: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #50: FLAVIN MONONUCLEOTIDE
+Macromolecule #51: POTASSIUM ION
+Macromolecule #52: CARDIOLIPIN
+Macromolecule #53: ZINC ION
+Macromolecule #54: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #55: MAGNESIUM ION
+Macromolecule #56: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #57: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
+Macromolecule #58: CHOLIC ACID
+Macromolecule #59: MYRISTIC ACID
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III Details: Sample was incubated on grid for 30 s before plunge freezing. | |||||||||
Details | Complex I proteoliposomes on a graphene-oxide coated gold grid with even liposome distribution. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
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: 1 / Number real images: 5568 / Average exposure time: 3.4 sec. / Average electron dose: 39.9 e/Å2 Details: The data were collected with aberration-free image shift (AFIS). |
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: 3.0 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 |