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Open data
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Basic information
Entry | Database: PDB / ID: 8b9z | |||||||||
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Title | Drosophila melanogaster complex I in the Active state (Dm1) | |||||||||
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![]() | OXIDOREDUCTASE / Mitochondrial complex I / Respiratory complex I / NADH:ubiquinone oxidoreductase / Ubiquinone | |||||||||
Function / homology | ![]() Mitochondrial protein import / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / RHOG GTPase cycle / Mitochondrial protein degradation / regulation of terminal button organization / Neutrophil degranulation / protein lipoylation ...Mitochondrial protein import / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / RHOG GTPase cycle / Mitochondrial protein degradation / regulation of terminal button organization / Neutrophil degranulation / protein lipoylation / deoxynucleoside kinase activity / cellular respiration / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / : / 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 / reactive oxygen species metabolic process / determination of adult lifespan / response to reactive oxygen species / mitochondrial intermembrane space / transmembrane transport / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial matrix / mitochondrion / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å | |||||||||
![]() | Agip, A.A. / Chung, I. / Sanchez-Martinez, A. / Whitworth, A.J. / Hirst, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of mitochondrial respiratory complex I from . Authors: Ahmed-Noor A Agip / Injae Chung / Alvaro Sanchez-Martinez / Alexander J Whitworth / Judy Hirst / ![]() Abstract: Respiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane. is a ...Respiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane. is a candidate model organism for complex I due to its high evolutionary conservation with the mammalian enzyme, well-developed genetic toolkit, and complex physiology for studies in specific cell types and tissues. Here, we isolate complex I from and determine its structure, revealing a 43-subunit assembly with high structural homology to its 45-subunit mammalian counterpart, including a hitherto unknown homologue to subunit NDUFA3. The major conformational state of the enzyme is the mammalian-type 'ready-to-go' active resting state, with a fully ordered and enclosed ubiquinone-binding site, but a subtly altered global conformation related to changes in subunit ND6. The mammalian-type 'deactive' pronounced resting state is not observed: in two minor states, the ubiquinone-binding site is unchanged, but a deactive-type π-bulge is present in ND6-TMH3. Our detailed structural knowledge of complex I provides a foundation for new approaches to disentangle mechanisms of complex I catalysis and regulation in bioenergetics and physiology. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 217.4 KB | Display | |
Data in CIF | ![]() | 325.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15936MC ![]() 8ba0C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules AHJKLMN
#1: Protein | Mass: 13572.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P18930, NADH:ubiquinone reductase (H+-translocating) |
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#8: Protein | Mass: 36383.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: C7DZL9, NADH:ubiquinone reductase (H+-translocating) |
#10: Protein | Mass: 19996.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P18933, NADH:ubiquinone reductase (H+-translocating) |
#11: Protein | Mass: 11363.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P18934, NADH:ubiquinone reductase (H+-translocating) |
#12: Protein | Mass: 65777.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: C7DZL4, NADH:ubiquinone reductase (H+-translocating) |
#13: Protein | Mass: 51473.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P18931, NADH:ubiquinone reductase (H+-translocating) |
#14: Protein | Mass: 39839.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P03896, NADH:ubiquinone reductase (H+-translocating) |
-Protein , 6 types, 7 molecules BDGTUbj
#2: Protein | Mass: 20493.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
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#4: Protein | Mass: 48880.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
#7: Protein | Mass: 78724.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q94511, NADH:ubiquinone reductase (H+-translocating) | ||||
#19: Protein | Mass: 9725.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #26: Protein | | Mass: 7376.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #33: Protein | | Mass: 7618.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+NADH dehydrogenase ... , 29 types, 29 molecules CEFIOPQRVWXYZadefghiklmnopqrs
-Non-polymers , 12 types, 39 molecules ![](data/chem/img/PC1.gif)
![](data/chem/img/3PE.gif)
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![](data/chem/img/NA.gif)
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![](data/chem/img/DGT.gif)
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![](data/chem/img/SF4.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/FES.gif)
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![](data/chem/img/DGT.gif)
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![](data/chem/img/ZN.gif)
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#43: Chemical | #44: Chemical | ChemComp-3PE / #45: Chemical | ChemComp-SF4 / #46: Chemical | ChemComp-CDL / #47: Chemical | #48: Chemical | ChemComp-FMN / | #49: Chemical | ChemComp-NA / | #50: Chemical | ChemComp-UQ9 / | #51: Chemical | ChemComp-DGT / | #52: Chemical | ChemComp-NDP / | #53: Chemical | ChemComp-ZN / | #54: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Mitochondrial respiratory complex I / Type: COMPLEX Details: Native purification of mitochondrial complex I from Drosophila melanogaster (fruit fly) W1118. Entity ID: #1-#42 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 1 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: Following glow discharge for 90 s at 20 mA, the grid was treated for 7 days in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ...Details: Following glow discharge for 90 s at 20 mA, the grid was treated for 7 days in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ethanol and dried prior to blotting Grid material: GOLD / Grid type: UltrAuFoil | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 10 seconds before plunging |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 41.88 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3082 |
Image scans | Movie frames/image: 40 |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 194538 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37608 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6ZR2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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