+Open data
-Basic information
Entry | Database: PDB / ID: 5j8k | ||||||
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Title | Architecture of supercomplex I-III2 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / membrane protein complex / supercomplex | ||||||
Function / homology | Function and homology information : / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / : / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / membrane => GO:0016020 / mitochondrial inner membrane ...: / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / : / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / membrane => GO:0016020 / mitochondrial inner membrane / electron transfer activity / ubiquitin protein ligase binding / heme binding / proteolysis / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å | ||||||
Authors | Letts, J.A. / Fiedorczuk, K. / Sazanov, L.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nature / Year: 2016 Title: The architecture of respiratory supercomplexes. Authors: James A Letts / Karol Fiedorczuk / Leonid A Sazanov / Abstract: Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) ...Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We identify two distinct arrangements of supercomplex CICIIICIV (the respirasome)-a major 'tight' form and a minor 'loose' form (resolved at the resolution of 5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex assembly or disassembly. We have also determined an architecture of supercomplex CICIII at 7.8 Å resolution. All observed density can be attributed to the known 80 subunits of the individual complexes, including 132 transmembrane helices. The individual complexes form tight interactions that vary between the architectures, with complex IV subunit COX7a switching contact from complex III to complex I. The arrangement of active sites within the supercomplex may help control reactive oxygen species production. To our knowledge, these are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5j8k.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5j8k.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5j8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/5j8k ftp://data.pdbj.org/pub/pdb/validation_reports/j8/5j8k | HTTPS FTP |
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-Related structure data
Related structure data | 8129MC 8128C 8130C 5j4zC 5j7yC 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
+Protein , 34 types, 39 molecules ABCDEFGHIJKLMNOPQSdTUVWXYabcef...
-Protein/peptide , 2 types, 2 molecules Rj
#18: Protein/peptide | Mass: 2486.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA |
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#35: Protein/peptide | Mass: 3762.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA |
-COMPLEX I B14. ... , 2 types, 2 molecules Zk
#26: Protein | Mass: 10145.497 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA |
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#36: Protein | Mass: 7081.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA |
-COMPLEX I UNKNOWN SUBUNIT FRAGMENT ... , 14 types, 15 molecules 012345678yxwvut
#37: Protein/peptide | Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA | ||||||||||||||||||||
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#38: Protein/peptide | Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA | ||||||||||||||||||||
#39: Protein/peptide | Mass: 3252.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA | ||||||||||||||||||||
#40: Protein/peptide | Mass: 2400.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA #41: Protein/peptide | | Mass: 2911.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA #42: Protein/peptide | | Mass: 1805.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA #43: Protein/peptide | | Mass: 3337.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA #44: Protein/peptide | | Mass: 2315.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA #45: Protein/peptide | | Mass: 3932.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA #46: Protein/peptide | | Mass: 1124.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA #47: Protein/peptide | | Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA #48: Protein/peptide | | Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA #49: Protein/peptide | | Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA #50: Protein/peptide | | Mass: 1039.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA |
-COMPLEX III SUBUNIT ... , 7 types, 14 molecules AAALABAMADAOAFAQAGARAJAUAKAV
#51: Protein | Mass: 49385.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5Q5G6 #52: Protein | Mass: 45189.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5Q0F9 #54: Protein | Mass: 27323.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5Q0A9 #56: Protein | Mass: 12949.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5P642 #57: Protein | Mass: 8884.331 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5PUP9 #60: Protein | Mass: 6937.975 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5P6B2 #61: Protein | Mass: 5932.946 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5PSD1 |
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-Cytochrome b-c1 complex subunit Rieske, ... , 2 types, 4 molecules AEAPAIAT
#55: Protein | Mass: 21654.607 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5P2X9, quinol-cytochrome-c reductase #59: Protein | Mass: 5824.802 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5P2X9, quinol-cytochrome-c reductase |
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-Non-polymers , 3 types, 16 molecules
#62: Chemical | ChemComp-SF4 / #63: Chemical | ChemComp-FES / #64: Chemical | ChemComp-HEM / |
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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: Supercomplex I-III2 / Type: COMPLEX Details: Supercomplex formed by respiratory complexes I and III Entity ID: #1-#62 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 1.4 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Ovis aries (sheep) / Organ: Heart / Organelle: mitochondria | ||||||||||||||||||||
Buffer solution | pH: 7.7 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Single particles dispersed in digitonin | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blotted 32 seconds |
-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: 47000 X / Calibrated magnification: 81395 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 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 |
Image recording | Average exposure time: 4 sec. / Electron dose: 34 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 1608 Details: Images were collected in movie mode with 17 frames per second |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 69 / Used frames/image: 1-32 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 67650 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9844 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL |