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Open data
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Basic information
Entry | Database: PDB / ID: 5ldw | ||||||
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Title | Structure of mammalian respiratory Complex I, class1 | ||||||
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![]() | OXIDOREDUCTASE / NADH:ubiquinone oxidoreductase / multienzyme complexes / Complex I / mitochondria | ||||||
Function / homology | ![]() Complex I biogenesis / RHOG GTPase cycle / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / Respiratory electron transport / gliogenesis / neural precursor cell proliferation / : / [2Fe-2S] cluster assembly / oxygen sensor activity ...Complex I biogenesis / RHOG GTPase cycle / cellular response to oxygen levels / mitochondrial large ribosomal subunit binding / Respiratory electron transport / gliogenesis / neural precursor cell proliferation / : / [2Fe-2S] cluster assembly / oxygen sensor activity / deoxynucleoside kinase activity / cellular respiration / Neutrophil degranulation / Mitochondrial protein degradation / NADH:ubiquinone reductase (H+-translocating) / apoptotic mitochondrial changes / 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 / negative regulation of intrinsic apoptotic signaling pathway / ATP metabolic process / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / neurogenesis / regulation of mitochondrial membrane potential / fatty acid binding / mitochondrial membrane / apoptotic signaling pathway / mitochondrial intermembrane space / negative regulation of cell growth / fatty acid biosynthetic process / 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 / mitochondrial matrix / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / mitochondrion / nucleoplasm / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.27 Å | ||||||
![]() | Vinothkumar, K.R. / Zhu, J. / Hirst, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of mammalian respiratory complex I. Authors: Jiapeng Zhu / Kutti R Vinothkumar / Judy Hirst / ![]() Abstract: Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive ...Complex I (NADH:ubiquinone oxidoreductase), one of the largest membrane-bound enzymes in the cell, powers ATP synthesis in mammalian mitochondria by using the reducing potential of NADH to drive protons across the inner mitochondrial membrane. Mammalian complex I (ref. 1) contains 45 subunits, comprising 14 core subunits that house the catalytic machinery (and are conserved from bacteria to humans) and a mammalian-specific cohort of 31 supernumerary subunits. Knowledge of the structures and functions of the supernumerary subunits is fragmentary. Here we describe a 4.2-Å resolution single-particle electron cryomicroscopy structure of complex I from Bos taurus. We have located and modelled all 45 subunits, including the 31 supernumerary subunits, to provide the entire structure of the mammalian complex. Computational sorting of the particles identified different structural classes, related by subtle domain movements, which reveal conformationally dynamic regions and match biochemical descriptions of the 'active-to-de-active' enzyme transition that occurs during hypoxia. Our structures therefore provide a foundation for understanding complex I assembly and the effects of mutations that cause clinically relevant complex I dysfunctions, give insights into the structural and functional roles of the supernumerary subunits and reveal new information on the mechanism and regulation of catalysis. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 163.3 KB | Display | |
Data in CIF | ![]() | 272.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4040MC ![]() 4032C ![]() 4041C ![]() 5lc5C ![]() 5ldxC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
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Components
-NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules AHJKLMN
#1: Protein | Mass: 13058.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Residues 28-50 are disordered or poor density / Source: (natural) ![]() ![]() References: UniProt: P03898, NADH:ubiquinone reductase (H+-translocating) |
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#8: Protein | Mass: 35688.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Residues 201-217 are disordered / Source: (natural) ![]() ![]() References: UniProt: P03887, NADH:ubiquinone reductase (H+-translocating) |
#10: Protein | Mass: 19082.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P03924, NADH:ubiquinone reductase (H+-translocating) |
#11: Protein | Mass: 10800.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P03902, NADH:ubiquinone reductase (H+-translocating) |
#12: Protein | Mass: 68327.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P03920, NADH:ubiquinone reductase (H+-translocating) |
#13: Protein | Mass: 52130.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P03910, NADH:ubiquinone reductase (H+-translocating) |
#14: Protein | Mass: 39274.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P03892, NADH:ubiquinone reductase (H+-translocating) |
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules BCDIQRe
#2: Protein | Mass: 20104.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: This chain coordinates an iron-sulphur cluster (SF4) Source: (natural) ![]() ![]() References: UniProt: P42026, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
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#3: Protein | Mass: 26464.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P23709, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
#4: Protein | Mass: 49165.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Residues 51-60 not modelled 129 is R for Cambridge cows instead of Q Source: (natural) ![]() ![]() References: UniProt: P17694, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
#9: Protein | Mass: 20219.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: This chain coordinates 2 iron-sulphur clusters (SF4) Source: (natural) ![]() ![]() References: UniProt: P42028, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
#17: Protein | Mass: 9634.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 8316.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: This chain coordinates a zinc atom / Source: (natural) ![]() ![]() |
#30: Protein | Mass: 12563.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules EFs
#5: Protein | Mass: 23840.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: This chain coordinates an iron-sulphur cluster (FES) Source: (natural) ![]() ![]() References: UniProt: P04394, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
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#6: Protein | Mass: 48562.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: This chain coordinates SF4 and also binds FMN / Source: (natural) ![]() ![]() References: UniProt: P25708, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
#44: Protein/peptide | Mass: 2996.685 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 3 molecules GTU
#7: Protein | Mass: 71847.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: This chain coordinates 2xSF4 and 1FES. We are uncertain of the register 210-692 Source: (natural) ![]() ![]() References: UniProt: P15690, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase |
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#20: Protein | Mass: 10119.541 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 12 molecules OPSVWXYZabqr
#15: Protein | Mass: 34256.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: We are uncertain of the register 5-90 / Source: (natural) ![]() ![]() |
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#16: Protein | Mass: 25549.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Residue range 187-199, 253-279 not modelled and none of the residues are assigned as the density doesn't allow it. The density for NAP is prominent and has been modelled. Source: (natural) ![]() ![]() |
#19: Protein | Mass: 11097.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#21: Protein | Mass: 13203.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#22: Protein | Mass: 15083.544 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: Protein | Mass: 18115.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#24: Protein | Mass: 14772.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#25: Protein | Mass: 14135.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#26: Protein | Mass: 8117.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#27: Protein | Mass: 7860.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#42: Protein | Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#43: Protein | Mass: 7422.140 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules cd
#28: Protein/peptide | Mass: 5836.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#29: Protein | Mass: 11988.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 11 types, 11 molecules fghijklmnop
#31: Protein | Mass: 6978.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#32: Protein | Mass: 14469.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#33: Protein | Mass: 12614.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#34: Protein | Mass: 10234.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#35: Protein | Mass: 4443.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#36: Protein | Mass: 6315.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#37: Protein | Mass: 10060.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#38: Protein | Mass: 13415.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#39: Protein | Mass: 19246.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#40: Protein | Mass: 16297.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#41: Protein | Mass: 16906.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 5 types, 11 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/ZN.gif)
#45: Chemical | ChemComp-SF4 / #46: Chemical | #47: Chemical | ChemComp-FMN / | #48: Chemical | ChemComp-NAP / | #49: Chemical | ChemComp-ZN / | |
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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: Bovine respiratory Complex I / Type: COMPLEX Details: Complex I is the first enzyme in the electron transport chain located in the inner membrane of mitochondria and in higher eukaryotes, it is a multi-subunit membrane protein complex, consisting of >40 subunits. Entity ID: #1-#44 / Source: NATURAL |
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Molecular weight | Value: 1 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 8 / Details: 20 mM TRIS-HCL, 150 mM NaCl, 0.03% CYMAL-7 |
Buffer component | Conc.: 150 mM / Name: sodium chloride / Formula: NaCl |
Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Enzyme was purified from bovine heart mitochondria. The detergent used for the final step is cymal-7. |
Specimen support | Details: Holey carbon grids were placed on a filter paper in a glass petridish and pumped for around 5 minutes to remove any residual moisture. The glow of the plasma was observed and glow discharge when it was purple. Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: The specimen was vitrified in an environmental plunge-freeze apparatus present in a cold room, blot for 12-15 seconds after the diameter of the blotted meniscus ceases to spread and plunged. |
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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: 59000 X / Calibrated magnification: 105263 X / Calibrated defocus min: 1800 nm / Calibrated defocus max: 5500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 87.5 K / Temperature (min): 87.5 K |
Image recording | Average exposure time: 2 sec. / Electron dose: 35 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) Details: Images were collected in movie mode at 17 frames per second. Thus each frame has ~1.0 e/A2 |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 34 / Used frames/image: 1-34 |
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Processing
Software | Name: REFMAC / Version: 5.8.0134 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: Each image was exposed for 2 seconds resulting in a total dose of ~35 e/A2s. The frames were captures with a in-house protocol at 17 frames/second. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: CTF correction wad done per particle after the CTF was estimated on the whole micrograph. Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 139456 / Details: All particles were picked manually | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48033 / Nominal pixel size: 1.33 Å / Actual pixel size: 1.33 Å / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 83.049 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: Maximum likelihood | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.27 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Total: 51117 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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