+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10815 | |||||||||
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Title | Structure of Yarrowia lipolytica complex I at 2.7 A | |||||||||
Map data | Global map | |||||||||
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) / Yarrowia lipolytica (strain CLIB 122 / E 150) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Hirst J / Grba D | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Mitochondrial complex I structure reveals ordered water molecules for catalysis and proton translocation. Authors: Daniel N Grba / Judy Hirst / Abstract: Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. ...Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. Recent cryo-EM analyses of mammalian and yeast complex I have revolutionized structural and mechanistic knowledge and defined structures in different functional states. Here, we describe a 2.7-Å-resolution structure of the 42-subunit complex I from the yeast Yarrowia lipolytica containing 275 structured water molecules. We identify a proton-relay pathway for ubiquinone reduction and water molecules that connect mechanistically crucial elements and constitute proton-translocation pathways through the membrane. By comparison with known structures, we deconvolute structural changes governing the mammalian 'deactive transition' (relevant to ischemia-reperfusion injury) and their effects on the ubiquinone-binding site and a connected cavity in ND1. Our structure thus provides important insights into catalysis by this enigmatic respiratory machine. | |||||||||
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_10815.map.gz | 325.9 MB | EMDB map data format | |
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Header (meta data) | emd-10815-v30.xml emd-10815.xml | 78.1 KB 78.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10815_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_10815.png | 76.1 KB | ||
Masks | emd_10815_msk_1.map | 347.6 MB | Mask map | |
Others | emd_10815_half_map_1.map.gz emd_10815_half_map_2.map.gz | 277.7 MB 277.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10815 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10815 | HTTPS FTP |
-Validation report
Summary document | emd_10815_validation.pdf.gz | 439.4 KB | Display | EMDB validaton report |
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Full document | emd_10815_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | emd_10815_validation.xml.gz | 21.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10815 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10815 | HTTPS FTP |
-Related structure data
Related structure data | 6yj4MC 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_10815.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Global map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.055 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10815_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_10815_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_10815_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Yarrowia lipolytica mitochondrial complex I (NADH:Ubiquinone oxid...
+Supramolecule #1: Yarrowia lipolytica mitochondrial complex I (NADH:Ubiquinone oxid...
+Supramolecule #2: Yarrowia lipolytica mitochondrial complex I
+Supramolecule #3: Entity 10
+Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3
+Macromolecule #2: Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #3: NUGM protein
+Macromolecule #4: NUCM protein
+Macromolecule #5: Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #6: Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #7: Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #8: NADH-ubiquinone oxidoreductase chain 1
+Macromolecule #9: Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #10: NADH-ubiquinone oxidoreductase chain 6
+Macromolecule #11: NADH-ubiquinone oxidoreductase chain 4L
+Macromolecule #12: NADH-ubiquinone oxidoreductase chain 5
+Macromolecule #13: NADH-ubiquinone oxidoreductase chain 4
+Macromolecule #14: NADH dehydrogenase subunit 2
+Macromolecule #15: Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #16: Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #17: Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #18: Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #19: Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #20: Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Com...
+Macromolecule #21: Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Com...
+Macromolecule #22: Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #23: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #24: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #25: Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #26: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #27: Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #28: subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #29: Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #30: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #31: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #32: Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #33: Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #34: subunit NUNM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #35: Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #36: subunit NIGM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #37: Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #38: Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #39: Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #40: Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #41: Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #42: Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
+Macromolecule #43: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
+Macromolecule #44: IRON/SULFUR CLUSTER
+Macromolecule #45: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #46: DIUNDECYL PHOSPHATIDYL CHOLINE
+Macromolecule #47: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #48: FLAVIN MONONUCLEOTIDE
+Macromolecule #49: CARDIOLIPIN
+Macromolecule #50: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #51: ZINC ION
+Macromolecule #52: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...
+Macromolecule #53: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.45 |
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Grid | Model: UltrAuFoil / Material: GOLD / Support film - Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Details: Gold grids pre-treated with PEG thiol reagent |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2540 / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: -2.7 µm / Calibrated defocus min: -1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |