+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4093 | |||||||||
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Title | Entire ovine respiratory complex I, Combined Map | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Complex I biogenesis / Respiratory electron transport / : / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / ubiquinone binding ...Complex I biogenesis / Respiratory electron transport / : / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / acyl binding / ubiquinone binding / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / ATP metabolic process / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / respiratory electron transport chain / reactive oxygen species metabolic process / regulation of mitochondrial membrane potential / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / apoptotic signaling pathway / electron transport chain / circadian rhythm / aerobic respiration / mitochondrial intermembrane space / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / membrane => GO:0016020 / mitochondrial inner membrane / mitochondrial matrix / negative regulation of DNA-templated transcription / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Ovis aries (sheep) / Sheep (sheep) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Fiedorczuk K / Letts JA / Sazanov LA | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nature / Year: 2016 Title: Atomic structure of the entire mammalian mitochondrial complex I. Authors: Karol Fiedorczuk / James A Letts / Gianluca Degliesposti / Karol Kaszuba / Mark Skehel / Leonid A Sazanov / Abstract: Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation ...Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation across the membrane. It is the largest protein assembly of the respiratory chain with a total mass of 970 kilodaltons. Here we present a nearly complete atomic structure of ovine (Ovis aries) mitochondrial complex I at 3.9 Å resolution, solved by cryo-electron microscopy with cross-linking and mass-spectrometry mapping experiments. All 14 conserved core subunits and 31 mitochondria-specific supernumerary subunits are resolved within the L-shaped molecule. The hydrophilic matrix arm comprises flavin mononucleotide and 8 iron-sulfur clusters involved in electron transfer, and the membrane arm contains 78 transmembrane helices, mostly contributed by antiporter-like subunits involved in proton translocation. Supernumerary subunits form an interlinked, stabilizing shell around the conserved core. Tightly bound lipids (including cardiolipins) further stabilize interactions between the hydrophobic subunits. Subunits with possible regulatory roles contain additional cofactors, NADPH and two phosphopantetheine molecules, which are shown to be involved in inter-subunit interactions. We observe two different conformations of the complex, which may be related to the conformationally driven coupling mechanism and to the active-deactive transition of the enzyme. Our structure provides insight into the mechanism, assembly, maturation and dysfunction of mitochondrial complex I, and allows detailed molecular analysis of disease-causing mutations. | |||||||||
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_4093.map.gz | 3 MB | EMDB map data format | |
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Header (meta data) | emd-4093-v30.xml emd-4093.xml | 61.3 KB 61.3 KB | Display Display | EMDB header |
Images | emd_4093.png | 88.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4093 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4093 | HTTPS FTP |
-Validation report
Summary document | emd_4093_validation.pdf.gz | 218.2 KB | Display | EMDB validaton report |
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Full document | emd_4093_full_validation.pdf.gz | 217.3 KB | Display | |
Data in XML | emd_4093_validation.xml.gz | 4.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4093 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4093 | HTTPS FTP |
-Related structure data
Related structure data | 5lnkMC 4084C 4090C 4091C C: citing same article (ref.) M: atomic model generated by this map |
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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_4093.map.gz / Format: CCP4 / Size: 14.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.39 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 complex I
+Supramolecule #1: Mitochondrial complex I
+Macromolecule #1: Mitochondrial complex I, 51 kDa subunit
+Macromolecule #2: Mitochondrial complex I, 24 kDa subunit
+Macromolecule #3: Mitochondrial complex I, 75 kDa subunit
+Macromolecule #4: Mitochondrial complex I, 49 kDa subunit
+Macromolecule #5: Mitochondrial complex I, 30 kDa subunit
+Macromolecule #6: Mitochondrial complex I, PSST subunit
+Macromolecule #7: Mitochondrial complex I, TYKY subunit
+Macromolecule #8: Mitochondrial complex I, ND1 subunit
+Macromolecule #9: Mitochondrial complex I, ND2 subunit
+Macromolecule #10: Mitochondrial complex I, ND3 subunit
+Macromolecule #11: Mitochondrial complex I, ND4 subunit
+Macromolecule #12: Mitochondrial complex I, ND4L subunit
+Macromolecule #13: Mitochondrial complex I, ND5 subunit
+Macromolecule #14: Mitochondrial complex I, ND6 subunit
+Macromolecule #15: Mitochondrial complex I, 10 kDa subunit
+Macromolecule #16: Mitochondrial complex I, 13 kDa subunit
+Macromolecule #17: Mitochondrial complex I, 18 kDa subunit
+Macromolecule #18: Mitochondrial complex I, 39 kDa subunit
+Macromolecule #19: Mitochondrial complex I, B8 subunit
+Macromolecule #20: Mitochondrial complex I, B13 subunit
+Macromolecule #21: Mitochondrial complex I, B14 subunit
+Macromolecule #22: Mitochondrial complex I, B14.5a subunit
+Macromolecule #23: Mitochondrial complex I, B17.2 subunit
+Macromolecule #24: Acyl carrier protein
+Macromolecule #25: Mitochondrial complex I, 42 kDa subunit
+Macromolecule #26: Mitochondrial complex I, 15 kDa subunit
+Macromolecule #27: Mitochondrial complex I, B9 subunit
+Macromolecule #28: Mitochondrial complex I, B12 subunit
+Macromolecule #29: Mitochondrial complex I, B14.5b subunit
+Macromolecule #30: Mitochondrial complex I, B15 subunit
+Macromolecule #31: Mitochondrial complex I, B16.6 subunit
+Macromolecule #32: Mitochondrial complex I, B17 subunit
+Macromolecule #33: Mitochondrial complex I, B18 subunit
+Macromolecule #34: Mitochondrial complex I, B22 subunit
+Macromolecule #35: Mitochondrial complex I, AGGG subunit
+Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...
+Macromolecule #37: Mitochondrial complex I, ESSS subunit
+Macromolecule #38: Mitochondrial complex I, KFYI subunit
+Macromolecule #39: Mitochondrial complex I, MNLL subunit
+Macromolecule #40: Mitochondrial complex I, MWFE subunit
+Macromolecule #41: Mitochondrial complex I, PDSW subunit
+Macromolecule #42: Mitochondrial complex I, PGIV subunit
+Macromolecule #43: Mitochondrial complex I, SGDH subunit
+Macromolecule #44: Mitochondrial complex I, B14.7 subunit
+Macromolecule #45: IRON/SULFUR CLUSTER
+Macromolecule #46: FLAVIN MONONUCLEOTIDE
+Macromolecule #47: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #48: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
+Macromolecule #49: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
+Macromolecule #50: CARDIOLIPIN
+Macromolecule #51: ZINC ION
+Macromolecule #52: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
+Macromolecule #53: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...
+Macromolecule #54: 4'-PHOSPHOPANTETHEINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 34s blotting. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-7 / Number grids imaged: 2 / Number real images: 2600 / Average exposure time: 1.0 sec. / Average electron dose: 26.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 100720 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Details: For the fourteen core subunits we used as a starting point our previous structure from T. thermophilus (PDB 4HEA) with sequence adjusted to ovine and side-chains rebuilt in SQWRL4. These are ...Details: For the fourteen core subunits we used as a starting point our previous structure from T. thermophilus (PDB 4HEA) with sequence adjusted to ovine and side-chains rebuilt in SQWRL4. These are chains 1, 2, 3, 4, 5, 6, 9, H, A, J, K, N, M and L (with the same chain IDs as in 4HEA). For the remaining supernumerary subunits it was mostly de novo building with some help from homology modeling, which in most cases was not very useful due to low sequence homology. In few cases models produced by Phyre2 server were useful and were used as a starting point, due to the presence of templates with high coverage and confidence: 42kDa (chain k) - PDB ID 1P6X (xray) 39kDa (chain d) - PDB ID 3WJ7 (xray) SDAPs (chains j and X) - PDB ID 2DNW (NMR) B8 (chain e) - PDB ID 1S3A (NMR) |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL |
Output model | PDB-5lnk: |