+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12741 | |||||||||
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Title | Cryo-EM structure of respiratory complex I under turnover | |||||||||
Map data | complex I under turnover, map postprocessed in region | |||||||||
Sample |
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Function / homology | Function and homology information NADH dehydrogenase / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / respiratory chain complex I / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding ...NADH dehydrogenase / oxidoreductase activity, acting on NAD(P)H / NADH:ubiquinone reductase (H+-translocating) / respiratory chain complex I / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / : / 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 / mitochondrial inner membrane / oxidoreductase activity / mitochondrion / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Yarrowia lipolytica (yeast) / Candida lipolytica (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Parey K / Vonck J | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Sci Adv / Year: 2021 Title: High-resolution structure and dynamics of mitochondrial complex I-Insights into the proton pumping mechanism. Authors: Kristian Parey / Jonathan Lasham / Deryck J Mills / Amina Djurabekova / Outi Haapanen / Etienne Galemou Yoga / Hao Xie / Werner Kühlbrandt / Vivek Sharma / Janet Vonck / Volker Zickermann / Abstract: Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1-MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes ...Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1-MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes substantially to the proton motive force that drives ATP synthase. Several structures of complex I from bacteria and mitochondria have been determined, but its catalytic mechanism has remained controversial. We here present the cryo-EM structure of complex I from at 2.1-Å resolution, which reveals the positions of more than 1600 protein-bound water molecules, of which ~100 are located in putative proton translocation pathways. Another structure of the same complex under steady-state activity conditions at 3.4-Å resolution indicates conformational transitions that we associate with proton injection into the central hydrophilic axis. By combining high-resolution structural data with site-directed mutagenesis and large-scale molecular dynamic simulations, we define details of the proton translocation pathways and offer insights into the redox-coupled proton pumping mechanism of complex I. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12741.map.gz | 227.2 MB | EMDB map data format | |
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Header (meta data) | emd-12741-v30.xml emd-12741.xml | 64.3 KB 64.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12741_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_12741.png | 166.5 KB | ||
Masks | emd_12741_msk_1.map | 244.1 MB | Mask map | |
Others | emd_12741_half_map_1.map.gz emd_12741_half_map_2.map.gz | 194.9 MB 194.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12741 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12741 | HTTPS FTP |
-Validation report
Summary document | emd_12741_validation.pdf.gz | 620.1 KB | Display | EMDB validaton report |
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Full document | emd_12741_full_validation.pdf.gz | 619.7 KB | Display | |
Data in XML | emd_12741_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | emd_12741_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12741 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12741 | HTTPS FTP |
-Related structure data
Related structure data | 7o6yMC 7o71C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12741.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | complex I under turnover, map postprocessed in region | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12741_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_12741_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_12741_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mitochondrial NADH:ubiquinone oxidoreductase
+Supramolecule #1: Mitochondrial NADH:ubiquinone oxidoreductase
+Macromolecule #1: Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #2: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
+Macromolecule #3: NUCM protein
+Macromolecule #4: Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #5: Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #6: Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #7: Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #9: Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #10: Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #12: NADH dehydrogenase subunit 2
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #14: Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #15: Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #16: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #17: subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #18: Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #19: Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #20: Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #21: Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #22: Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #23: Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Com...
+Macromolecule #24: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #25: Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Com...
+Macromolecule #26: Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #27: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #28: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #29: Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #30: Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #31: Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #32: Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #33: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #34: Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #35: Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #36: Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #37: Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #38: Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #39: Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #40: Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #41: Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #42: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #43: IRON/SULFUR CLUSTER
+Macromolecule #44: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #45: FLAVIN MONONUCLEOTIDE
+Macromolecule #46: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
+Macromolecule #47: Ubiquinone-9
+Macromolecule #48: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #49: DIUNDECYL PHOSPHATIDYL CHOLINE
+Macromolecule #50: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #51: Phosphatidylinositol
+Macromolecule #52: CARDIOLIPIN
+Macromolecule #53: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #54: Lauryl Maltose Neopentyl Glycol
+Macromolecule #55: ZINC ION
+Macromolecule #56: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
-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: 7.2 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 283 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 K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 4776 / Average exposure time: 8.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.2 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |