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Yorodumi- EMDB-4873: Cryo-EM structure of respiratory complex I from Yarrowia lipolyti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4873 | |||||||||
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Title | Cryo-EM structure of respiratory complex I from Yarrowia lipolytica at 3.2 A resolution | |||||||||
Map data | complex I from Yarrowia lipolytica | |||||||||
Sample |
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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) / Candida lipolytica (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Parey K / Vonck J | |||||||||
Funding support | Germany, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4873.map.gz | 338.4 MB | EMDB map data format | |
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Header (meta data) | emd-4873-v30.xml emd-4873.xml | 60.3 KB 60.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4873_fsc.xml | 16.1 KB | Display | FSC data file |
Images | emd_4873.png | 146.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4873 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4873 | HTTPS FTP |
-Validation report
Summary document | emd_4873_validation.pdf.gz | 259 KB | Display | EMDB validaton report |
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Full document | emd_4873_full_validation.pdf.gz | 258.2 KB | Display | |
Data in XML | emd_4873_validation.xml.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4873 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4873 | HTTPS FTP |
-Related structure data
Related structure data | 6rfrMC 4872C 4874C 6rfqC 6rfsC 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_4873.map.gz / Format: CCP4 / Size: 361.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | complex I from Yarrowia lipolytica | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.077 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-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: Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #3: Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #4: Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #5: Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #6: Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #7: Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #8: Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #9: Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #10: Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #11: Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #12: Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #13: Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #14: Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Com...
+Macromolecule #15: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #16: Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Com...
+Macromolecule #17: Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #18: Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #19: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #20: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #21: Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #22: Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #23: Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #24: Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #25: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #26: Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #27: Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #28: Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #29: Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #30: Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #31: Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #32: Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #33: Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #34: Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #35: Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #36: Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #37: Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #38: Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #39: Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #40: Subunit NU6M 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: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
+Macromolecule #47: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #48: CARDIOLIPIN
+Macromolecule #49: Lauryl Maltose Neopentyl Glycol
+Macromolecule #50: DIUNDECYL PHOSPHATIDYL CHOLINE
+Macromolecule #51: ZINC ION
+Macromolecule #52: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #53: Ubiquinone-9
+Macromolecule #54: Phosphatidylinositol
+Macromolecule #55: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: C-flat-1/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
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: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 4043 / 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 | Calibrated magnification: 46425 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |