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- PDB-8b6h: Cryo-EM structure of cytochrome c oxidase dimer (complex IV) from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b6h | |||||||||||||||
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Title | Cryo-EM structure of cytochrome c oxidase dimer (complex IV) from respiratory supercomplex of Tetrahymena thermophila | |||||||||||||||
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![]() | ELECTRON TRANSPORT / Ciliate / mitochondrial / supercomplex | |||||||||||||||
Function / homology | ![]() thiosulfate transmembrane transporter activity / oxaloacetate transmembrane transporter activity / malate transmembrane transporter activity / protein maturation by [2Fe-2S] cluster transfer / succinate transmembrane transporter activity / sulfate transmembrane transporter activity / mitochondrial cytochrome c oxidase assembly / phosphate ion transmembrane transport / : / cytochrome-c oxidase ...thiosulfate transmembrane transporter activity / oxaloacetate transmembrane transporter activity / malate transmembrane transporter activity / protein maturation by [2Fe-2S] cluster transfer / succinate transmembrane transporter activity / sulfate transmembrane transporter activity / mitochondrial cytochrome c oxidase assembly / phosphate ion transmembrane transport / : / cytochrome-c oxidase / antiporter activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / transmembrane transporter activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / 2 iron, 2 sulfur cluster binding / protein transport / mitochondrial inner membrane / DNA-binding transcription factor activity / copper ion binding / heme binding / endoplasmic reticulum / mitochondrion / membrane / nucleus / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||||||||
![]() | Muhleip, A. / Kock Flygaard, R. / Amunts, A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of mitochondrial membrane bending by the I-II-III-IV supercomplex. Authors: Alexander Mühleip / Rasmus Kock Flygaard / Rozbeh Baradaran / Outi Haapanen / Thomas Gruhl / Victor Tobiasson / Amandine Maréchal / Vivek Sharma / Alexey Amunts / ![]() ![]() ![]() ![]() ![]() Abstract: Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes ...Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III-IV supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization. #1: ![]() Title: Structural basis of mitochondrial membrane bending by I-II-III2-IV2 supercomplex Authors: Muhleip, A. / Flygaard, R.K. / Haapanen, O. / Baradaran, R. / Gruhl, T. / Tobiasson, V. / Marechal, A. / Sharma, V. / Amunts, A. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 8.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 15867MC ![]() 8b6fC ![]() 8b6gC ![]() 8b6jC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Cytochrome c oxidase subunit ... , 3 types, 6 molecules DADaDBDbDDDd
#1: Protein | Mass: 80578.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 72388.883 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 75431.312 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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+Protein , 34 types, 68 molecules DCDcDFDfDKDkDNDnDODoDPDpDQDqDSDsDUDuDVDvDWDwDXDxDYDyDZDzEAEa...
-Transmembrane protein, ... , 12 types, 24 molecules DEDeDGDgDHDhDJDjDMDmDRDrEBEbEHEhELElEMEmEOEoEQEq
#5: Protein | Mass: 15618.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 12786.321 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #8: Protein | Mass: 16427.672 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | Mass: 26601.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | Mass: 57814.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #17: Protein | Mass: 41307.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #27: Protein | Mass: 24701.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #33: Protein | Mass: 20388.264 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #37: Protein | Mass: 18801.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #38: Protein | Mass: 18600.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #40: Protein | Mass: 15588.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #42: Protein | Mass: 14344.524 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-NADH dehydrogenase [ubiquinone] 1 ... , 2 types, 4 molecules DIDiDTDt
#9: Protein | Mass: 28666.662 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #19: Protein | Mass: 37552.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Zf-Tim10 DDP domain-containing ... , 2 types, 4 molecules ETEtEXEx
#45: Protein | Mass: 10435.701 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #49: Protein | Mass: 8354.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 15 types, 245 molecules ![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/LPP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/UQ8.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/LPP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/UQ8.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
#54: Chemical | ChemComp-HEA / #55: Chemical | #56: Chemical | #57: Chemical | ChemComp-CDL / #58: Chemical | ChemComp-PC1 / #59: Chemical | ChemComp-3PE / #60: Chemical | ChemComp-LPP / #61: Chemical | #62: Chemical | #63: Chemical | #64: Chemical | ChemComp-K / | #65: Chemical | ChemComp-UQ8 / #66: Chemical | #67: Chemical | ChemComp-FES / #68: Chemical | |
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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 |
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Sample preparation
Component | Name: Cytochrome c oxidase dimer (complex-IV) from respiratory supercomplex of Tetrahymena thermophila Type: COMPLEX / Entity ID: #1-#53 / Source: NATURAL |
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Molecular weight | Value: 3.2 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 25.66 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138746 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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