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Yorodumi- PDB-6gcs: Cryo-EM structure of respiratory complex I from Yarrowia lipolytica -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gcs | ||||||
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Title | Cryo-EM structure of respiratory complex I from Yarrowia lipolytica | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Complex I / NADH dehydrogenase / Mitochondrion Proton pumping / Ubiquinone | ||||||
Function / homology | Function and homology information lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / protein import into mitochondrial matrix / mitochondrial [2Fe-2S] assembly complex / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / respiratory chain complex I / iron-sulfur cluster assembly / ubiquinone binding ...lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / protein import into mitochondrial matrix / mitochondrial [2Fe-2S] assembly complex / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / respiratory chain complex I / iron-sulfur cluster assembly / ubiquinone binding / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / acyl binding / acyl carrier activity / 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 / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / 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: 4.32 Å | ||||||
Authors | Parey, K. / Vonck, J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Elife / Year: 2018 Title: Cryo-EM structure of respiratory complex I at work. Authors: Kristian Parey / Ulrich Brandt / Hao Xie / Deryck J Mills / Karin Siegmund / Janet Vonck / Werner Kühlbrandt / Volker Zickermann / Abstract: Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 ...Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons from NADH to ubiquinone, providing the energy to drive proton pumping at distant sites in the membrane arm. The critical steps of energy conversion are associated with the redox chemistry of ubiquinone. We report the cryo-EM structure of complete mitochondrial complex I from the aerobic yeast both in the deactive form and after capturing the enzyme during steady-state activity. The site of ubiquinone binding observed during turnover supports a two-state stabilization change mechanism for 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 | 6gcs.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6gcs.ent.gz | 1008 KB | Display | PDB format |
PDBx/mmJSON format | 6gcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gcs_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6gcs_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6gcs_validation.xml.gz | 177.4 KB | Display | |
Data in CIF | 6gcs_validation.cif.gz | 280.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/6gcs ftp://data.pdbj.org/pub/pdb/validation_reports/gc/6gcs | HTTPS FTP |
-Related structure data
Related structure data | 4384MC 4385C 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 , 41 types, 41 molecules ABCDEFGHIJKLMOPQRSUWXYZabcdfgh...
-Protein/peptide , 1 types, 1 molecules e
#28: Protein/peptide | Mass: 3847.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Polyalanine / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating) |
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-Non-polymers , 8 types, 16 molecules
#43: Chemical | ChemComp-SF4 / #44: Chemical | #45: Chemical | ChemComp-FMN / | #46: Chemical | ChemComp-NDP / | #47: Chemical | ChemComp-ZN / | #48: Chemical | ChemComp-ZMP / | #49: Chemical | ChemComp-CDL / | #50: Chemical | |
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-Details
Has protein modification | Y |
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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: 963.7 kDa/nm / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Yarrowia lipolytica (yeast) | |||||||||||||||||||||||||
Buffer solution | pH: 7.2 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: C-flat-1/1 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: OTHER / Nominal magnification: 200000 X / Calibrated magnification: 45872 X / Nominal defocus max: -3 nm / Nominal defocus min: -1.5 nm / Cs: 2 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 8 sec. / Electron dose: 60.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3110 |
EM imaging optics | Energyfilter name: GIF Bioquantum |
Image scans | Movie frames/image: 40 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 271443 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124626 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.32 Å | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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