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Yorodumi- EMDB-4874: Cryo-EM structure of a respiratory complex I mutant lacking NDUFS4 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4874 | |||||||||
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Title | Cryo-EM structure of a respiratory complex I mutant lacking NDUFS4 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial [2Fe-2S] assembly complex / protein import into mitochondrial matrix / ubiquinone-6 biosynthetic process / respiratory chain complex I / cellular respiration / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster assembly ...lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial [2Fe-2S] assembly complex / protein import into mitochondrial matrix / ubiquinone-6 biosynthetic process / respiratory chain complex I / cellular respiration / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster assembly / 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 / mitochondrial inner membrane / 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: 4.04 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_4874.map.gz | 337.7 MB | EMDB map data format | |
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Header (meta data) | emd-4874-v30.xml emd-4874.xml | 56 KB 56 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4874_fsc.xml | 16.1 KB | Display | FSC data file |
Images | emd_4874.png | 135.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4874 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4874 | HTTPS FTP |
-Validation report
Summary document | emd_4874_validation.pdf.gz | 311 KB | Display | EMDB validaton report |
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Full document | emd_4874_full_validation.pdf.gz | 310.1 KB | Display | |
Data in XML | emd_4874_validation.xml.gz | 13.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4874 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4874 | HTTPS FTP |
-Related structure data
Related structure data | 6rfsMC 4872C 4873C 6rfqC 6rfrC 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_4874.map.gz / Format: CCP4 / Size: 361.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.09 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 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 NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #23: Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #24: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #25: Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #26: Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #27: Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #28: Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #29: Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #30: Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #31: Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #32: Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #33: Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #34: Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #35: Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #36: Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #37: Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #38: Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #39: Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #40: Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #41: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #42: IRON/SULFUR CLUSTER
+Macromolecule #43: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #44: FLAVIN MONONUCLEOTIDE
+Macromolecule #45: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #46: ZINC ION
+Macromolecule #47: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.7 mg/mL | |||||||||||||||
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Buffer | pH: 7.2 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI POLARA 300 |
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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 grids imaged: 1 / Number real images: 5964 / Average exposure time: 8.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 45872 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -2.0 µm / Nominal magnification: 200000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-6rfs: |