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Yorodumi- PDB-7tgh: Cryo-EM structure of respiratory super-complex CI+III2 from Tetra... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 7tgh | ||||||
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| Title | Cryo-EM structure of respiratory super-complex CI+III2 from Tetrahymena thermophila | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Mitochondrial respiration / Electron transport chain / Oxidoreductase / Super-complex CI+III2 | ||||||
| Function / homology | Function and homology informationlipid-A-disaccharide synthase / lipid-A-disaccharide synthase activity / quinol-cytochrome-c reductase / NADH:ubiquinone reductase (H+-translocating) / membrane protein complex / P450-containing electron transport chain / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / mitochondrial electron transport, ubiquinol to cytochrome c ...lipid-A-disaccharide synthase / lipid-A-disaccharide synthase activity / quinol-cytochrome-c reductase / NADH:ubiquinone reductase (H+-translocating) / membrane protein complex / P450-containing electron transport chain / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / mitochondrial electron transport, ubiquinol to cytochrome c / lipid A biosynthetic process / ligase activity / electron transport coupled proton transport / acyl binding / NADH:ubiquinone reductase (H+-translocating) / acyl carrier activity / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / catalytic complex / quinone binding / ATP synthesis coupled electron transport / protein folding chaperone / aerobic respiration / respiratory electron transport chain / electron transport chain / phospholipid binding / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / NAD binding / metallopeptidase activity / unfolded protein binding / FMN binding / protein-folding chaperone binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / electron transfer activity / mitochondrial inner membrane / ribosome / heme binding / protein-containing complex binding / mitochondrion / zinc ion binding / metal ion binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Zhou, L. / Maldonado, M. / Padavannil, A. / Guo, F. / Letts, J.A. | ||||||
| Funding support | United States, 1items
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Citation | Journal: Science / Year: 2022Title: Structures of 's respiratory chain reveal the diversity of eukaryotic core metabolism. Authors: Long Zhou / María Maldonado / Abhilash Padavannil / Fei Guo / James A Letts / ![]() Abstract: Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multisubunit complexes in the inner mitochondrial membrane. To probe the functional and ...Respiration is a core biological energy-converting process whose last steps are carried out by a chain of multisubunit complexes in the inner mitochondrial membrane. To probe the functional and structural diversity of eukaryotic respiration, we examined the respiratory chain of the ciliate (Tt). Using cryo-electron microscopy on a mixed sample, we solved structures of a supercomplex between Tt complex I (Tt-CI) and Tt-CIII (Tt-SC I+III) and a structure of Tt-CIV. Tt-SC I+III (~2.3 megadaltons) is a curved assembly with structural and functional symmetry breaking. Tt-CIV is a ~2.7-megadalton dimer with more than 50 subunits per protomer, including mitochondrial carriers and a TIM8-TIM13-like domain. Our structural and functional study of the respiratory chain reveals divergence in key components of eukaryotic respiration, thereby expanding our understanding of core metabolism. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 7tgh.cif.gz | 3.4 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb7tgh.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 7tgh.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/7tgh ftp://data.pdbj.org/pub/pdb/validation_reports/tg/7tgh | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 25882MC ![]() 7w5zC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
| EM raw data | EMPIAR-10919 (Title: Single particle cryogenic electron micrographs of tetrahymena mitochondrial electron transport chain complexesData size: 7.8 TB Data #1: Unaligned multiframe micrographs of Tetrahymena respiratory chain complexes - Krios data [micrographs - multiframe] Data #2: Non-dose weighted motion corrected micrographs of Tetrahymena respiratory chain complexes - Krios data [micrographs - single frame] Data #3: Dose-weighted motion corrected micrographs of Tetrahymena respiratory chain complexes - Krios data [micrographs - single frame]) |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-NADH-ubiquinone oxidoreductase ... , 7 types, 7 molecules 134X1S1S8V2
| #1: Protein | Mass: 32636.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q950Y3, NADH:ubiquinone reductase (H+-translocating) |
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| #5: Protein | Mass: 14416.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q950Z7, NADH:ubiquinone reductase (H+-translocating) |
| #19: Protein | Mass: 58690.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q950X9, NADH:ubiquinone reductase (H+-translocating) |
| #46: Protein | Mass: 17381.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #50: Protein | Mass: 80580.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #56: Protein | Mass: 28053.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #62: Protein | Mass: 31216.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-NADH dehydrogenase subunit ... , 6 types, 6 molecules 1B2B5S2S3S7
| #2: Protein | Mass: 7238.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #4: Protein | Mass: 20899.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q951B2, NADH:ubiquinone reductase (H+-translocating) |
| #21: Protein | Mass: 88179.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q950Z0, NADH:ubiquinone reductase (H+-translocating) |
| #51: Protein | Mass: 51227.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q951B1, NADH:ubiquinone reductase (H+-translocating) |
| #52: Protein | Mass: 23803.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q950Z4, NADH:ubiquinone reductase (H+-translocating) |
| #55: Protein | Mass: 18324.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q951B4, NADH:ubiquinone reductase (H+-translocating) |
+Protein , 45 types, 52 molecules 23A3a3B3b3C3c3D3d3E3e3F3f3G3g4L5B6A2A5A6A7A9AMB7B8BLCC3J1...
-Transmembrane protein, ... , 13 types, 16 molecules 3H3h3I3i3J3jTDT5TBBMANP1B3A3TET7
| #13: Protein | Mass: 15677.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | Mass: 14262.554 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #15: Protein | Mass: 7455.741 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #40: Protein | | Mass: 8787.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #48: Protein | | Mass: 23971.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #60: Protein | | Mass: 13340.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #64: Protein | | Mass: 24419.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #66: Protein | | Mass: 26545.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #72: Protein | | Mass: 29389.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #73: Protein | | Mass: 9942.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #78: Protein | | Mass: 15831.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #80: Protein | | Mass: 8445.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() #81: Protein | | Mass: 16909.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Protein/peptide , 3 types, 3 molecules 3M3l3m
| #16: Protein/peptide | Mass: 2181.579 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #17: Protein/peptide | Mass: 1781.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #18: Protein/peptide | Mass: 1725.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Acyl carrier ... , 2 types, 2 molecules ABAC
| #29: Protein | Mass: 16249.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #30: Protein | Mass: 15428.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-NADH dehydrogenase [ubiquinone] ... , 3 types, 3 molecules ALS4V1
| #31: Protein | Mass: 22890.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #53: Protein | Mass: 21642.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #61: Protein | Mass: 52313.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q23KE4, NADH:ubiquinone reductase (H+-translocating) |
-Gamma-carbonic ... , 2 types, 2 molecules C1C2
| #37: Protein | Mass: 28216.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #38: Protein | Mass: 25395.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 13 types, 104 molecules 
























| #82: Chemical | ChemComp-CDL / #83: Chemical | ChemComp-PC1 / #84: Chemical | ChemComp-HEM / #85: Chemical | #86: Chemical | #87: Chemical | ChemComp-FES / #88: Chemical | ChemComp-3PE / #89: Chemical | #90: Chemical | ChemComp-NDP / | #91: Chemical | ChemComp-ZMP / | #92: Chemical | ChemComp-ADP / | #93: Chemical | ChemComp-SF4 / #94: Chemical | ChemComp-FMN / | |
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-Details
| Has ligand of interest | Y |
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| Has protein modification | Y |
-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 Super-complex I+III2 of Tetrahymena thermophila Type: COMPLEX / Entity ID: #1-#81 / Source: NATURAL | |||||||||||||||||||||||||
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| Molecular weight | Value: 2.3 MDa / Experimental value: NO | |||||||||||||||||||||||||
| Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
| Buffer solution | pH: 7.4 Details: Solution were made fresh from concentrated stocks, filtered and de-gassed before equilibration onto Superose6 column | |||||||||||||||||||||||||
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| Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
| Specimen support | Details: 30 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
| Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: incubation time before blotting: 60s, blot time: 9s, blot force: 25, offset: -2, incubation after blotting: 0s |
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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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 58616 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
| Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Image recording | Average exposure time: 5.9 sec. / Electron dose: 66.69 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7895 |
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Processing
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
| Particle selection | Num. of particles selected: 1144671 | ||||||||||||||||||||||||||||||||||||||||
| Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
| 3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203834 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
| Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
| Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 49.81 Å2 | ||||||||||||||||||||||||||||||||||||||||
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FIELD EMISSION GUN