+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10711 | |||||||||
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Title | Cryo-EM structure of a respiratory complex I F89A mutant | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex I / NADH dehydrogenase / Mitochondrion proton pumping / Ubiquinone / Oxidoreductase | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
Authors | Parey K / Vonck J | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Essential role of accessory subunit LYRM6 in the mechanism of mitochondrial complex I. Authors: Etienne Galemou Yoga / Kristian Parey / Amina Djurabekova / Outi Haapanen / Karin Siegmund / Klaus Zwicker / Vivek Sharma / Volker Zickermann / Heike Angerer / Abstract: Respiratory complex I catalyzes electron transfer from NADH to ubiquinone (Q) coupled to vectorial proton translocation across the inner mitochondrial membrane. Despite recent progress in structure ...Respiratory complex I catalyzes electron transfer from NADH to ubiquinone (Q) coupled to vectorial proton translocation across the inner mitochondrial membrane. Despite recent progress in structure determination of this very large membrane protein complex, the coupling mechanism is a matter of ongoing debate and the function of accessory subunits surrounding the canonical core subunits is essentially unknown. Concerted rearrangements within a cluster of conserved loops of central subunits NDUFS2 (β1-β2 loop), ND1 (TMH5-6 loop) and ND3 (TMH1-2 loop) were suggested to be critical for its proton pumping mechanism. Here, we show that stabilization of the TMH1-2 loop by accessory subunit LYRM6 (NDUFA6) is pivotal for energy conversion by mitochondrial complex I. We determined the high-resolution structure of inactive mutant F89A of eukaryotic complex I from the yeast Yarrowia lipolytica and found long-range structural changes affecting the entire loop cluster. In atomistic molecular dynamics simulations of the mutant, we observed conformational transitions in the loop cluster that disrupted a putative pathway for delivery of substrate protons required in Q redox chemistry. Our results elucidate in detail the essential role of accessory subunit LYRM6 for the function of eukaryotic complex I and offer clues on its redox-linked proton pumping mechanism. | |||||||||
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_10711.map.gz | 227.7 MB | EMDB map data format | |
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Header (meta data) | emd-10711-v30.xml emd-10711.xml | 63.8 KB 63.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10711_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_10711.png | 184.4 KB | ||
Filedesc metadata | emd-10711.cif.gz | 14.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10711 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10711 | HTTPS FTP |
-Validation report
Summary document | emd_10711_validation.pdf.gz | 658.5 KB | Display | EMDB validaton report |
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Full document | emd_10711_full_validation.pdf.gz | 658.1 KB | Display | |
Data in XML | emd_10711_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | emd_10711_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10711 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10711 | HTTPS FTP |
-Related structure data
Related structure data | 6y79MC 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_10711.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 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: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #47: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #48: Lauryl Maltose Neopentyl Glycol
+Macromolecule #49: ZINC ION
+Macromolecule #50: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #51: DIUNDECYL PHOSPHATIDYL CHOLINE
+Macromolecule #52: CARDIOLIPIN
+Macromolecule #53: Ubiquinone-9
+Macromolecule #54: Phosphatidylinositol
+Macromolecule #55: (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)MET...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL | |||||||||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||||||||
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: 30 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number real images: 2016 / Average exposure time: 3.0 sec. / Average electron dose: 51.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | 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: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |