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- PDB-2ybb: Fitted model for bovine mitochondrial supercomplex I1III2IV1 by s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ybb | ||||||
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Title | Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876) | ||||||
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![]() | OXIDOREDUCTASE / SUPERCOMPLEX B / MITOCHONDRIA / RESPIRATORY CHAIN / AMPHIPOL A8-35 / RANDOM CONICAL TILT | ||||||
Function / homology | ![]() Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly ...Release of apoptotic factors from the mitochondria / Formation of apoptosome / Activation of caspases through apoptosome-mediated cleavage / Pyroptosis / Regulation of the apoptosome activity / Transcriptional activation of mitochondrial biogenesis / Detoxification of Reactive Oxygen Species / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / respiratory chain complex IV assembly / : / NADH:ubiquinone reductase (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / mitochondrial respirasome assembly / respiratory chain complex IV / : / regulation of oxidative phosphorylation / Respiratory electron transport / : / cytochrome-c oxidase / : / oxidative phosphorylation / quinol-cytochrome-c reductase / molybdopterin cofactor binding / respiratory chain complex I / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / iron-sulfur cluster assembly / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / NADH dehydrogenase activity / : / ubiquinone binding / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / respiratory electron transport chain / ferric iron binding / central nervous system development / mitochondrial membrane / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / electron transfer activity / iron ion binding / copper ion binding / apoptotic process / heme binding / mitochondrion / proteolysis / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 19 Å | ||||||
![]() | Althoff, T. / Mills, D.J. / Popot, J.-L. / Kuehlbrandt, W. | ||||||
![]() | ![]() Title: Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1. Authors: Thorsten Althoff / Deryck J Mills / Jean-Luc Popot / Werner Kühlbrandt / ![]() Abstract: The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. ...The respiratory chain in the inner mitochondrial membrane contains three large multi-enzyme complexes that together establish the proton gradient for ATP synthesis, and assemble into a supercomplex. A 19-Å 3D map of the 1.7-MDa amphipol-solubilized supercomplex I(1)III(2)IV(1) from bovine heart obtained by single-particle electron cryo-microscopy reveals an amphipol belt replacing the membrane lipid bilayer. A precise fit of the X-ray structures of complex I, the complex III dimer, and monomeric complex IV indicates distances of 13 nm between the ubiquinol-binding sites of complexes I and III, and of 10-11 nm between the cytochrome c binding sites of complexes III and IV. The arrangement of respiratory chain complexes suggests two possible pathways for efficient electron transfer through the supercomplex, of which the shorter branch through the complex III monomer proximal to complex I may be preferred. #1: ![]() Title: Strukturelle Untersuchungen Am Superkomplex I1III2Iv1 Der Atmungskette Mittels Kryoelektronenmikroskopie Authors: Althoff, T. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Download
PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | 1.4 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 201.7 KB | Display | |
Data in CIF | ![]() | 342.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1876MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-NADH-QUINONE OXIDOREDUCTASE SUBUNIT ... , 10 types, 10 molecules 12345678op
#1: Protein | Mass: 48693.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NQO1 (51KDA) / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 20309.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NQO2 (24KDA) / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 86656.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NQO3 (75KDA) / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 46428.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NQO4 (49KDA) / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 23893.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NQO5 (30KDA) / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 20262.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NQO6 (PSST) / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 14812.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NQO15 / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 20106.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NQO9 (TYKY) / Source: (natural) ![]() ![]() |
#36: Protein | Mass: 32187.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SUBUNIT NUON (CHAIN2) / Source: (natural) ![]() ![]() |
#37: Protein | Mass: 23932.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SUBUNITS NUOA, J AND K (CHAIN3,6 AND 4L) / Source: (natural) ![]() ![]() |
-CYTOCHROME B-C1 COMPLEX SUBUNIT ... , 9 types, 18 molecules AaBbEeFfGgHhIiJjKk
#9: Protein | Mass: 49266.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 46575.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 21640.580 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 13371.190 Da / Num. of mol.: 2 / Mutation: YES / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | Mass: 9606.027 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | Mass: 9189.116 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein | Mass: 6677.736 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein | Mass: 7209.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | Mass: 6370.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 4 types, 6 molecules CcDdRY
#11: Protein | Mass: 42620.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 27323.277 Da / Num. of mol.: 2 / Fragment: RESIDUES 85-325 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #26: Protein | | Mass: 9452.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #33: Protein | | Mass: 11595.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-CYTOCHROME C OXIDASE SUBUNIT ... , 12 types, 12 molecules LMNOPQSTUVWX
#20: Protein | Mass: 57065.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#21: Protein | Mass: 26040.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#22: Protein | Mass: 29957.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: Protein | Mass: 17179.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#24: Protein | Mass: 12453.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#25: Protein | Mass: 10684.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#27: Protein | Mass: 10039.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#28: Protein | Mass: 8494.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#29: Protein | Mass: 6682.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#30: Protein | Mass: 6365.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#31: Protein/peptide | Mass: 5449.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#32: Protein/peptide | Mass: 4967.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH\: UBIQUINONE OXIDOREDUCTASE, MEMBRANE SUBUNIT ... , 2 types, 2 molecules mn
#34: Protein | Mass: 40357.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SUBUNIT NUOL (CHAIN5) / Source: (natural) ![]() ![]() |
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#35: Protein | Mass: 33293.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SUBUNIT NUOM (CHAIN4) / Source: (natural) ![]() ![]() |
-Non-polymers , 15 types, 1640 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/SMA.gif)
![](data/chem/img/UQ1.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/NAI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/SMA.gif)
![](data/chem/img/UQ1.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#38: Chemical | ChemComp-SF4 / #39: Chemical | ChemComp-FMN / | #40: Chemical | ChemComp-NAI / | #41: Chemical | ChemComp-MG / #42: Chemical | ChemComp-FES / #43: Chemical | ChemComp-CA / | #44: Chemical | ChemComp-HEM / #45: Chemical | #46: Chemical | #47: Chemical | #48: Chemical | ChemComp-CDL / #49: Chemical | #50: Chemical | #51: Chemical | ChemComp-ZN / | #52: Water | ChemComp-HOH / | |
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-Details
Sequence details | DUE TO THE AMBIGUITY ABOUT THE REGISTER OF THE SEQUENCE, THESE CHAINS WERE BUILT WITH UNK RESIDUES ...DUE TO THE AMBIGUITY ABOUT THE REGISTER OF THE SEQUENCE, THESE CHAINS WERE BUILT WITH UNK RESIDUES ONLY. THE UNIPROT REFERENCES |
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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: RESPIRATORY SUPERCOMPLEX B (I1III2IV1) COMPOSED OF COMPLEX I, DIMERIC COMPLEX III AND COMPLEX IV FROM BOVINE HEART MITOCHONDRIA Type: COMPLEX Details: THE SUPERCOMPLEXES WERE KEPT SOLUBLE BY AMPHIPOLS A8-35 |
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Buffer solution | Name: 10 MM KCL, 15 MM HEPES, RESIDUAL TREHALOSE / pH: 7.7 / Details: 10 MM KCL, 15 MM HEPES, RESIDUAL TREHALOSE |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 70, TEMPERATURE- 95, INSTRUMENT- CUSTOM-MADE HAND PLUNGER, METHOD- ONE- SIDED BLOTTING FOR 26 - 30 SECONDS BEFORE PLUNGING, DETAILS- SAMPLE WAS ...Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 70, TEMPERATURE- 95, INSTRUMENT- CUSTOM-MADE HAND PLUNGER, METHOD- ONE- SIDED BLOTTING FOR 26 - 30 SECONDS BEFORE PLUNGING, DETAILS- SAMPLE WAS ADSORBED TO CARBON FILM FOR 30 SECONDS BEFORE BLOTTING |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 Details: LOW DOSE CONDITIONS. FOR RANDOM CONICAL TILT EACH AREA WAS IMAGED TWICE WITH THE FIRST IMAGE TAKEN AT A TILT ANGLE OF -45 OR -50 DEGREE |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 58829 X / Nominal defocus max: 6000 nm / Nominal defocus min: 500 nm / Cs: 2 mm |
Specimen holder | Temperature: 78 K / Tilt angle max: 0 ° / Tilt angle min: -50 ° |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 154 |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: PHASE-FLIPPPING ON EACH PARTICLE | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Method: RANDOM CONICAL TILT AND PROJECTION MATCHING WITH DIRECT FOURIER BACKPROJECTION AND SIRT Resolution: 19 Å / Num. of particles: 10684 / Nominal pixel size: 4.76 Å / Actual pixel size: 4.76 Å Details: FINAL MAP WAS CALCULATED WITH SIRT FROM COMBINED TILTED AND UNTILTED DATASETS WITH 10684 PARTICLES EACH AND OMITTING 30 PER CENT OF IMAGES WITH LOWEST CROSS CORRELATION. THIS ENTRY IS BASED ...Details: FINAL MAP WAS CALCULATED WITH SIRT FROM COMBINED TILTED AND UNTILTED DATASETS WITH 10684 PARTICLES EACH AND OMITTING 30 PER CENT OF IMAGES WITH LOWEST CROSS CORRELATION. THIS ENTRY IS BASED ON PDBS 3IAM,3M9C,1PP9,1BGY,1OCC AND 2B4Z WHICH WERE FITTED MANUALLY INTO THE EM DENSITY MAP OF BOVINE SUPERCOMPLEX I1III2IV1. THE POSITION OF 2B4Z WAS INFERRED FROM PDB 3CX5. THE CHAIN NAMES ARE CASE SENSITIVE. CHAINS A-K AND a-k DENOTE IDENTICAL CHAINS WITHIN A DIMER. CHAINS L-X AND M-P BELONG TO DIFFERENT PROTEINS. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1876. Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY | |||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 19 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 19 Å
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