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- EMDB-4872: Cryo-EM structure of a respiratory complex I assembly intermediat... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4872 | |||||||||
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Title | Cryo-EM structure of a respiratory complex I assembly intermediate with NDUFAF2 | |||||||||
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Function / homology | ![]() lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / mitochondrial [2Fe-2S] assembly complex / protein import into mitochondrial matrix / respiratory chain complex I / cellular respiration / ubiquinone-6 biosynthetic process / 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 / respiratory chain complex I / cellular respiration / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster assembly / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / mitochondrial electron transport, NADH to ubiquinone / : / ubiquinone binding / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / quinone binding / electron transport coupled proton transport / 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 / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / oxidoreductase activity / electron transfer activity / protein-containing complex binding / mitochondrion / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Parey K / Vonck J | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 338.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 57.2 KB 57.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.1 KB | Display | ![]() |
Images | ![]() | 145.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 296.5 KB | Display | ![]() |
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Full document | ![]() | 295.6 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rfqMC ![]() 4873C ![]() 4874C ![]() 6rfrC ![]() 6rfsC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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Sample components
+Entire : Complex I assembly intermediate
+Supramolecule #1: Complex I assembly intermediate
+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: Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Com...
+Macromolecule #14: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #15: Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Com...
+Macromolecule #16: Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #17: Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #18: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #19: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #20: Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #21: Subunit NUYM 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 N7BML assembly factor
+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: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
+Macromolecule #47: Lauryl Maltose Neopentyl Glycol
+Macromolecule #48: CARDIOLIPIN
+Macromolecule #49: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #50: DIUNDECYL PHOSPHATIDYL CHOLINE
+Macromolecule #51: Phosphatidylinositol
+Macromolecule #52: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.2 |
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Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
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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: 1386 / Average exposure time: 8.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 46425 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | ![]() PDB-6rfq: |