+Open data
-Basic information
Entry | Database: PDB / ID: 5ldx | ||||||
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Title | Structure of mammalian respiratory Complex I, class3. | ||||||
Components |
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Keywords | OXIDOREDUCTASE / NADH:ubiquinone oxidoreductase / multienzyme complexes / Complex I / mitochondria | ||||||
Function / homology | Function and homology information 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 / cellular respiration / Neutrophil degranulation / 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 / neurogenesis / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / 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 / fatty acid binding / NADH dehydrogenase (ubiquinone) activity / apoptotic signaling pathway / mitochondrial membrane / aerobic respiration / mitochondrial intermembrane space / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial inner membrane / mitochondrial matrix / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / mitochondrion / nucleoplasm / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 Å | ||||||
Authors | Vinothkumar, K.R. / Zhu, J. / Hirst, J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nature / Year: 2016 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. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 5ldx.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ldx.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 5ldx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ldx_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5ldx_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5ldx_validation.xml.gz | 164 KB | Display | |
Data in CIF | 5ldx_validation.cif.gz | 273.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/5ldx ftp://data.pdbj.org/pub/pdb/validation_reports/ld/5ldx | HTTPS FTP |
-Related structure data
Related structure data | 4041MC 4032C 4040C 5lc5C 5ldwC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 / Source: (natural) Bos taurus (cattle) 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 / Source: (natural) Bos taurus (cattle) 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) Bos taurus (cattle) 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) Bos taurus (cattle) 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 Details: Note: The density for transverse helix and the last TM helix around 548-605 is poor but has been left as observed for class 1 for comparison. Source: (natural) Bos taurus (cattle) 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) Bos taurus (cattle) 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) Bos taurus (cattle) 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 a Iron-sulphur cluster. / Source: (natural) Bos taurus (cattle) 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) Bos taurus (cattle) 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: 128 should be an R instead of Q for Cambridge cows. Source: (natural) Bos taurus (cattle) 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 2x SF4 / Source: (natural) Bos taurus (cattle) 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) Bos taurus (cattle) |
#18: Protein | Mass: 8316.853 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23934 |
#30: Protein | Mass: 12694.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02379 |
-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 FES / Source: (natural) Bos taurus (cattle) 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 1SF4 and binds FMN / Source: (natural) Bos taurus (cattle) 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) Bos taurus (cattle) |
-Protein , 2 types, 3 molecules GTU
#7: Protein | Mass: 64614.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: This chain coordinates 2 SF4 and 1FES / Source: (natural) Bos taurus (cattle) 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) Bos taurus (cattle) / References: UniProt: P52505 |
-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 12 types, 12 molecules OPSVWXYZabqr
#15: Protein | Mass: 34014.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P34942 |
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#16: Protein | Mass: 24102.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: binds NAP / Source: (natural) Bos taurus (cattle) |
#19: Protein | Mass: 11097.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02370 |
#21: Protein | Mass: 13203.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23935 |
#22: Protein | Mass: 14952.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02366 |
#23: Protein | Mass: 17617.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P42029 |
#24: Protein | Mass: 14640.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The density for this subunit is poor and the model has been taken from class1 for comparison. Source: (natural) Bos taurus (cattle) / References: UniProt: Q8HXG6 |
#25: Protein | Mass: 14135.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q95KV7 |
#26: Protein | Mass: 8117.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02377 |
#27: Protein | Mass: 7860.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02371 |
#42: Protein | Mass: 16309.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: O97725 |
#43: Protein | Mass: 7422.140 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) |
-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) Bos taurus (cattle) / References: UniProt: Q02376 |
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#29: Protein | Mass: 11988.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02827 |
-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) Bos taurus (cattle) / References: UniProt: Q02378 |
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#32: Protein | Mass: 14469.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q8HXG5 |
#33: Protein | Mass: 12614.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02380 |
#34: Protein | Mass: 10234.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02367 |
#35: Protein | Mass: 4443.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) |
#36: Protein | Mass: 6315.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) |
#37: Protein | Mass: 10060.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) |
#38: Protein | Mass: 13415.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P48305 |
#39: Protein | Mass: 19246.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02369 |
#40: Protein | Mass: 7583.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02368 |
#41: Protein | Mass: 16906.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q02373 |
-Non-polymers , 5 types, 11 molecules
#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 |
-Sample preparation
Component | Name: Bovine 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: Bos taurus (cattle) / Cellular location: Mitochondria / Organ: Heart / Organelle: Mitochondria |
Buffer solution | Name: 20 mM TRIS-HCL, 150 mM NaCl, 0.03% CYMAL-7 / pH: 8 |
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 discharged 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, blot for 12-15 seconds after the diameter of the blotted meniscus ceases to spread and plunged. |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 105263 X / Nominal defocus max: 5500 nm / Nominal defocus min: 1800 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): 85 K / Temperature (min): 85 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/A2s |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 34 / Used frames/image: 1-34 |
-Processing
Software | Name: PHENIX / Version: 1.10_2155: / 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 was corrected per particle. 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: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19306 / Nominal pixel size: 1.33 Å / Actual pixel size: 1.33 Å / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: The model from Class1 (D_1200000497) was used for rigid body fitting. The B-factor for individual atoms is carried over from class 1 and doesn't mean anything. |