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Yorodumi- PDB-7tgh: Cryo-EM structure of respiratory super-complex CI+III2 from Tetra... -
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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 information lipid-A-disaccharide synthase / lipid-A-disaccharide synthase activity / NADH:ubiquinone reductase (H+-translocating) / quinol-cytochrome-c reductase / medium-chain fatty acid-CoA ligase activity / P450-containing electron transport chain / protein processing involved in protein targeting to mitochondrion / ubiquinone-6 biosynthetic process / : / oxidoreductase activity, acting on NAD(P)H ...lipid-A-disaccharide synthase / lipid-A-disaccharide synthase activity / NADH:ubiquinone reductase (H+-translocating) / quinol-cytochrome-c reductase / medium-chain fatty acid-CoA ligase activity / P450-containing electron transport chain / protein processing involved in protein targeting to mitochondrion / ubiquinone-6 biosynthetic process / : / oxidoreductase activity, acting on NAD(P)H / ubiquinol-cytochrome-c reductase activity / lipid A biosynthetic process / mitochondrial electron transport, ubiquinol to cytochrome c / ubiquinone binding / chloroplast thylakoid membrane / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / electron transport coupled proton transport / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / quinone binding / : / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / chloroplast / mitochondrion organization / fatty acid metabolic process / mitochondrial membrane / electron transport chain / phospholipid binding / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / electron transfer activity / oxidoreductase activity / ribosome / heme binding / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / mitochondrion / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||
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: 2022 Title: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-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
Summary document | 7tgh_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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Full document | 7tgh_full_validation.pdf.gz | 4.4 MB | Display | |
Data in XML | 7tgh_validation.xml.gz | 381.6 KB | Display | |
Data in CIF | 7tgh_validation.cif.gz | 622.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/7tgh ftp://data.pdbj.org/pub/pdb/validation_reports/tg/7tgh | HTTPS FTP |
-Related structure data
Related structure data | 25882MC 7w5zC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-10919 (Title: Single particle cryogenic electron micrographs of tetrahymena mitochondrial electron transport chain complexes Data 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]) |
-Links
-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) Tetrahymena thermophila (eukaryote) / Strain: SB255 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) Tetrahymena thermophila (eukaryote) / Strain: SB255 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) Tetrahymena thermophila (eukaryote) / Strain: SB255 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) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: I7LT42 |
#50: Protein | Mass: 80580.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: Q23KA9 |
#56: Protein | Mass: 28053.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: I7MDW5 |
#62: Protein | Mass: 31216.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: I7MEP0 |
-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) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: Q09FB0 |
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#4: Protein | Mass: 20899.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 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) Tetrahymena thermophila (eukaryote) / Strain: SB255 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) Tetrahymena thermophila (eukaryote) / Strain: SB255 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) Tetrahymena thermophila (eukaryote) / Strain: SB255 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) Tetrahymena thermophila (eukaryote) / Strain: SB255 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) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: I7M484 #14: Protein | Mass: 14262.554 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: I7MM45 #15: Protein | Mass: 7455.741 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: I7MFL6 #40: Protein | | Mass: 8787.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: Q22DC2 #48: Protein | | Mass: 23971.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: I7LT77 #60: Protein | | Mass: 13340.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: Q22T55 #64: Protein | | Mass: 24419.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: Q22Z32 #66: Protein | | Mass: 26545.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: Q24F24 #72: Protein | | Mass: 29389.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: Q24C39 #73: Protein | | Mass: 9942.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: A4VD20 #78: Protein | | Mass: 15831.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: I7M9B3 #80: Protein | | Mass: 8445.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: I7MIK1 #81: Protein | | Mass: 16909.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: Q22HE4 |
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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) Tetrahymena thermophila (eukaryote) / Strain: SB255 |
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#17: Protein/peptide | Mass: 1781.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 |
#18: Protein/peptide | Mass: 1725.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 |
-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) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: Q22XT6 |
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#30: Protein | Mass: 15428.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: I7MD12 |
-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) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: A4VDQ6 |
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#53: Protein | Mass: 21642.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: I7MK61 |
#61: Protein | Mass: 52313.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 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) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: Q22XU5 |
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#38: Protein | Mass: 25395.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / Strain: SB255 / References: UniProt: I7M6S0 |
-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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-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: 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: Tetrahymena thermophila (eukaryote) / Strain: SB255 | |||||||||||||||||||||||||
Buffer solution | pH: 7.4 Details: Solution were made fresh from concentrated stocks, filtered and de-gassed before equilibration onto Superose6 column | |||||||||||||||||||||||||
Buffer component |
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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 |
-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 |
-Processing
Software |
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EM software |
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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 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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