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Yorodumi- PDB-6rfs: Cryo-EM structure of a respiratory complex I mutant lacking NDUFS4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rfs | ||||||
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Title | Cryo-EM structure of a respiratory complex I mutant lacking NDUFS4 | ||||||
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 / mitochondrial iron-sulfur cluster assembly complex / protein import into mitochondrial matrix / ubiquinone-6 biosynthetic process / NADH dehydrogenase activity / respiratory chain complex I / cellular respiration / oxidoreductase activity, acting on NAD(P)H ...lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial iron-sulfur cluster assembly complex / protein import into mitochondrial matrix / ubiquinone-6 biosynthetic process / NADH dehydrogenase activity / respiratory chain complex I / cellular respiration / oxidoreductase activity, acting on NAD(P)H / ubiquinone binding / acyl binding / electron transport coupled proton transport / iron-sulfur cluster assembly / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / 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: 4.04 Å | ||||||
Authors | Parey, K. / Vonck, J. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Sci Adv / Year: 2019 Title: High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease. Authors: Kristian Parey / Outi Haapanen / Vivek Sharma / Harald Köfeler / Thomas Züllig / Simone Prinz / Karin Siegmund / Ilka Wittig / Deryck J Mills / Janet Vonck / Werner Kühlbrandt / Volker Zickermann / Abstract: Respiratory complex I is a redox-driven proton pump, accounting for a large part of the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I dysfunction is ...Respiratory complex I is a redox-driven proton pump, accounting for a large part of the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I dysfunction is associated with severe human diseases. Assembly of the one-megadalton complex I in the inner mitochondrial membrane requires assembly factors and chaperones. We have determined the structure of complex I from the aerobic yeast by electron cryo-microscopy at 3.2-Å resolution. A ubiquinone molecule was identified in the access path to the active site. The electron cryo-microscopy structure indicated an unusual lipid-protein arrangement at the junction of membrane and matrix arms that was confirmed by molecular simulations. The structure of a complex I mutant and an assembly intermediate provide detailed molecular insights into the cause of a hereditary complex I-linked disease and complex I assembly in the inner mitochondrial membrane. | ||||||
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 | 6rfs.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6rfs.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6rfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/6rfs ftp://data.pdbj.org/pub/pdb/validation_reports/rf/6rfs | HTTPS FTP |
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-Related structure data
Related structure data | 4874MC 4872C 4873C 6rfqC 6rfrC 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 , 39 types, 39 molecules ABCDEFGHIJKLMPRSUWXZabcdefghij...
-Acyl carrier protein ... , 2 types, 2 molecules OQ
#14: Protein | Mass: 12053.585 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PXT9, UniProt: Q6C926*PLUS |
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#16: Protein | Mass: 14444.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NG21, UniProt: Q6C7X2*PLUS |
-Non-polymers , 6 types, 12 molecules
#42: Chemical | ChemComp-SF4 / #43: Chemical | #44: Chemical | ChemComp-FMN / | #45: Chemical | ChemComp-NDP / | #46: Chemical | ChemComp-ZN / | #47: Chemical | ChemComp-ZMP / | |
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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-#41 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Value: 1 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Yarrowia lipolytica (yeast) | |||||||||||||||||||||||||
Buffer solution | pH: 7.2 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2.7 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: 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: BRIGHT FIELDBright-field microscopy / Nominal magnification: 200000 X / Calibrated magnification: 45872 X / Nominal defocus max: -3000 nm / Nominal defocus min: -2000 nm / Cs: 2 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 8 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5964 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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: 418740 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145767 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.04 Å | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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