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Yorodumi- EMDB-14797: CryoEM structure of mitochondrial complex I from Chaetomium therm... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14797 | |||||||||
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Title | CryoEM structure of mitochondrial complex I from Chaetomium thermophilum (state 1) | |||||||||
Map data | Density modified map (Terwilliger et al., 2020) | |||||||||
Sample |
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Function / homology | Function and homology information nuclease activity / ubiquinone-6 biosynthetic process / single-stranded DNA helicase activity / oxidoreductase activity, acting on NAD(P)H / respiratory chain complex I / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / NADH dehydrogenase activity / : / mitochondrial electron transport, NADH to ubiquinone ...nuclease activity / ubiquinone-6 biosynthetic process / single-stranded DNA helicase activity / oxidoreductase activity, acting on NAD(P)H / respiratory chain complex I / NADH:ubiquinone reductase (H+-translocating) / ubiquinone binding / NADH dehydrogenase activity / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / NADH dehydrogenase (ubiquinone) activity / quinone binding / : / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / electron transport chain / mitochondrial intermembrane space / fatty acid biosynthetic process / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / DNA helicase / response to oxidative stress / DNA replication / mitochondrial inner membrane / DNA repair / protein-containing complex binding / mitochondrion / DNA binding / ATP binding / membrane / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.44 Å | |||||||||
Authors | Laube E / Kuehlbrandt W | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Sci Adv / Year: 2022 Title: Conformational changes in mitochondrial complex I of the thermophilic eukaryote . Authors: Eike Laube / Jakob Meier-Credo / Julian D Langer / Werner Kühlbrandt / Abstract: Mitochondrial complex I is a redox-driven proton pump that generates proton-motive force across the inner mitochondrial membrane, powering oxidative phosphorylation and ATP synthesis in eukaryotes. ...Mitochondrial complex I is a redox-driven proton pump that generates proton-motive force across the inner mitochondrial membrane, powering oxidative phosphorylation and ATP synthesis in eukaryotes. We report the structure of complex I from the thermophilic fungus , determined by cryoEM up to 2.4-Å resolution. We show that the complex undergoes a transition between two conformations, which we refer to as state 1 and state 2. The conformational switch is manifest in a twisting movement of the peripheral arm relative to the membrane arm, but most notably in substantial rearrangements of the Q-binding cavity and the E-channel, resulting in a continuous aqueous passage from the E-channel to subunit ND5 at the far end of the membrane arm. The conformational changes in the complex interior resemble those reported for mammalian complex I, suggesting a highly conserved, universal mechanism of coupling electron transport to proton pumping. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14797.map.gz | 68.4 MB | EMDB map data format | |
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Header (meta data) | emd-14797-v30.xml emd-14797.xml | 72.1 KB 72.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14797_fsc.xml | 20.4 KB | Display | FSC data file |
Images | emd_14797.png | 99.5 KB | ||
Others | emd_14797_additional_1.map.gz emd_14797_half_map_1.map.gz emd_14797_half_map_2.map.gz | 390 MB 720.5 MB 720.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14797 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14797 | HTTPS FTP |
-Validation report
Summary document | emd_14797_validation.pdf.gz | 821.3 KB | Display | EMDB validaton report |
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Full document | emd_14797_full_validation.pdf.gz | 820.9 KB | Display | |
Data in XML | emd_14797_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | emd_14797_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14797 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14797 | HTTPS FTP |
-Related structure data
Related structure data | 7zmgMC 7zm7C 7zm8C 7zmbC 7zmeC 7zmhC 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_14797.map.gz / Format: CCP4 / Size: 73.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Density modified map (Terwilliger et al., 2020) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unmodified/unsharpened map
File | emd_14797_additional_1.map | ||||||||||||
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Annotation | Unmodified/unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EM half map B
File | emd_14797_half_map_1.map | ||||||||||||
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Annotation | EM_half_map_B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EM half map A
File | emd_14797_half_map_2.map | ||||||||||||
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Annotation | EM_half_map_A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mitochondrial NADH:ubiquinone oxidoreductase in LMNG
+Supramolecule #1: Mitochondrial NADH:ubiquinone oxidoreductase in LMNG
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #2: NADH dehydrogenase subunit 2
+Macromolecule #3: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #4: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #5: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #6: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #7: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
+Macromolecule #8: Subunit NDUFS5 of NADH-ubiquinone oxidoreductase (Complex I)
+Macromolecule #9: NADH-ubiquinone oxidoreductase-like protein
+Macromolecule #10: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #11: NADH-ubiquinone oxidoreductase 49 kDa subunit-like protein
+Macromolecule #12: Subunit NDUFA1 of NADH-ubiquinone oxidoreductase (Complex I)
+Macromolecule #13: NADH dehydrogenase (Ubiquinone)-like protein
+Macromolecule #14: NADH-ubiquinone oxidoreductase-like protein
+Macromolecule #15: NADH-ubiquinone oxidoreductase 30.4 kDa subunit-like protein
+Macromolecule #16: Subunit NDUFV2 of NADH-ubiquinone oxidoreductase (Complex I)
+Macromolecule #17: Oxidoreductase-like protein
+Macromolecule #18: NADH-ubiquinone oxidoreductase-like protein
+Macromolecule #19: NADH-ubiquinone oxidoreductase-like protein
+Macromolecule #20: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #21: NADH-ubiquinone oxidoreductase-like protein
+Macromolecule #22: Acyl carrier protein
+Macromolecule #23: NADH-ubiquinone oxidoreductase B14 subunit-like protein
+Macromolecule #24: Complex I-B22
+Macromolecule #25: Complex I-ESSS
+Macromolecule #26: NADH-ubiquinone oxidoreductase
+Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
+Macromolecule #28: NADH-ubiquinone oxidoreductase-like protein
+Macromolecule #29: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
+Macromolecule #30: NADH-ubiquinone oxidoreductase-like protein
+Macromolecule #31: NADH dehydrogenase (Ubiquinone)-like protein
+Macromolecule #32: Subunit NDUFC2 of NADH-ubiquinone oxidoreductase (Complex I)
+Macromolecule #33: Subunit NDUFB3 of NADH-ubiquinone oxidoreductase (Complex I)
+Macromolecule #34: Subunit NDUFB10 of NADH-ubiquinone oxidoreductase (Complex I)
+Macromolecule #35: Subunit NDUFB2 of NADH-ubiquinone oxidoreductase (Complex I)
+Macromolecule #36: NADH dehydrogenase-like protein
+Macromolecule #37: Subunit NDUFA3 of NADH-ubiquinone oxidoreductase (Complex I)
+Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit
+Macromolecule #39: Subunit NDUFB6 of NADH-ubiquinone oxidoreductase (Complex I)
+Macromolecule #40: Subunit NDUFB4 of NADH-ubiquinone oxidoreductase (Complex I)
+Macromolecule #41: Subunit NDUFB5 of NADH-ubiquinone oxidoreductase (Complex I)
+Macromolecule #42: Oxidoreductase-like domain-containing protein
+Macromolecule #43: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #44: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #45: CARDIOLIPIN
+Macromolecule #46: Lauryl Maltose Neopentyl Glycol
+Macromolecule #47: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #48: IRON/SULFUR CLUSTER
+Macromolecule #49: FLAVIN MONONUCLEOTIDE
+Macromolecule #50: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #51: ZINC ION
+Macromolecule #52: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #53: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6503 / Average exposure time: 2.11 sec. / Average electron dose: 45.0 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: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |