+Open data
-Basic information
Entry | Database: PDB / ID: 7o6y | ||||||
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Title | Cryo-EM structure of respiratory complex I under turnover | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Complex I / NADH dehydrogenase / Mitochondrion proton pumping / Ubiquinone | ||||||
Function / homology | Function and homology information NADH dehydrogenase / ubiquinone-6 biosynthetic process / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding ...NADH dehydrogenase / ubiquinone-6 biosynthetic process / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / respiratory electron transport chain / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / electron transport chain / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / protein-containing complex binding / mitochondrion / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Yarrowia lipolytica (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Parey, K. / Vonck, J. | ||||||
Funding support | Germany, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7o6y.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7o6y.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7o6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o6y_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 7o6y_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 7o6y_validation.xml.gz | 226.3 KB | Display | |
Data in CIF | 7o6y_validation.cif.gz | 329.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/7o6y ftp://data.pdbj.org/pub/pdb/validation_reports/o6/7o6y | HTTPS FTP |
-Related structure data
Related structure data | 12741MC 7o71C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Protein , 34 types, 34 molecules ACGHIKSj45gDEFJMPRUWXYZabcdefh...
-NADH dehydrogenase ... , 2 types, 2 molecules B2
#2: Protein | Mass: 53829.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) References: UniProt: Q9UUU2, NADH:ubiquinone reductase (H+-translocating) |
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#12: Protein | Mass: 53381.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) References: UniProt: S5U4R9, NADH:ubiquinone reductase (H+-translocating) |
-NADH-ubiquinone oxidoreductase chain ... , 4 types, 4 molecules L136
#8: Protein | Mass: 9843.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) References: UniProt: S5U4U1, NADH:ubiquinone reductase (H+-translocating) |
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#11: Protein | Mass: 38389.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) References: UniProt: S5U3V2, NADH:ubiquinone reductase (H+-translocating) |
#13: Protein | Mass: 14506.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) References: UniProt: S5TMS4, NADH:ubiquinone reductase (H+-translocating) |
#16: Protein | Mass: 20793.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) References: UniProt: S5U3X7, NADH:ubiquinone reductase (H+-translocating) |
-Acyl carrier protein ... , 2 types, 2 molecules OQ
#23: Protein | Mass: 12053.585 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PXT9 |
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#25: Protein | Mass: 14444.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NG21 |
-Non-polymers , 14 types, 49 molecules
#43: Chemical | ChemComp-SF4 / #44: Chemical | #45: Chemical | ChemComp-FMN / | #46: Chemical | ChemComp-NAI / | #47: Chemical | ChemComp-UQ9 / | #48: Chemical | ChemComp-3PE / #49: Chemical | ChemComp-PLC / #50: Chemical | ChemComp-CPL / | #51: Chemical | #52: Chemical | ChemComp-CDL / #53: Chemical | ChemComp-NDP / | #54: Chemical | #55: Chemical | ChemComp-ZN / | #56: Chemical | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mitochondrial NADH:ubiquinone oxidoreductase / Type: COMPLEX / Entity ID: #1-#42 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Value: 1 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Yarrowia lipolytica (yeast) / Strain: GB30 | |||||||||||||||||||||||||
Buffer solution | pH: 7.2 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: -3200 nm / Nominal defocus min: -800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4776 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 30 eV |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 124092 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54863 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 30 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6RFR |