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Yorodumi- PDB-6rfr: Cryo-EM structure of respiratory complex I from Yarrowia lipolyti... -
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-Basic information
Entry | Database: PDB / ID: 6rfr | ||||||
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Title | Cryo-EM structure of respiratory complex I from Yarrowia lipolytica at 3.2 A resolution | ||||||
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 / cellular respiration / respiratory chain complex I / iron-sulfur cluster assembly ...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 / cellular respiration / 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: 3.2 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 | 6rfr.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6rfr.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6rfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rfr_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 6rfr_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 6rfr_validation.xml.gz | 208.8 KB | Display | |
Data in CIF | 6rfr_validation.cif.gz | 323.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/6rfr ftp://data.pdbj.org/pub/pdb/validation_reports/rf/6rfr | HTTPS FTP |
-Related structure data
Related structure data | 4873MC 4872C 4874C 6rfqC 6rfsC 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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-Components
+Protein , 40 types, 40 molecules ABCDEFGHIJKLMPRSUWXYZabcdefghi...
-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 , 13 types, 49 molecules
#43: Chemical | ChemComp-SF4 / #44: Chemical | #45: Chemical | ChemComp-FMN / | #46: Chemical | ChemComp-3PE / #47: Chemical | ChemComp-NDP / | #48: Chemical | ChemComp-CDL / #49: Chemical | #50: Chemical | ChemComp-PLC / #51: Chemical | ChemComp-ZN / | #52: Chemical | #53: Chemical | ChemComp-UQ9 / | #54: Chemical | ChemComp-T7X / #55: Chemical | ChemComp-CPL / | |
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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.: 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: 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: 130000 X / Calibrated magnification: 46425 X / Nominal defocus max: -2500 nm / Nominal defocus min: -1500 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: 4043 |
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: 666666 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 297066 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6GCS | ||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.2 Å | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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