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- PDB-8b6f: Cryo-EM structure of NADH:ubiquinone oxidoreductase (complex-I) f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b6f | |||||||||||||||
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Title | Cryo-EM structure of NADH:ubiquinone oxidoreductase (complex-I) from respiratory supercomplex of Tetrahymena thermophila | |||||||||||||||
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![]() | ELECTRON TRANSPORT / Ciliate / mitochondrial / complex-I / supercomplex | |||||||||||||||
Function / homology | ![]() NADH:ubiquinone reductase (H+-translocating) / lipid-A-disaccharide synthase / lipid-A-disaccharide synthase activity / medium-chain fatty acid-CoA ligase activity / P450-containing electron transport chain / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / lipid A biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity ...NADH:ubiquinone reductase (H+-translocating) / lipid-A-disaccharide synthase / lipid-A-disaccharide synthase activity / medium-chain fatty acid-CoA ligase activity / P450-containing electron transport chain / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / lipid A biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / mitochondrial electron transport, NADH to ubiquinone / : / chloroplast thylakoid membrane / ubiquinone binding / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / quinone binding / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / mitochondrion organization / fatty acid metabolic process / chloroplast / mitochondrial membrane / electron transport chain / phospholipid binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / ribosome / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / mitochondrion / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 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 | ![]() | 5.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.6 MB | Display | ![]() |
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Full document | ![]() | 4.8 MB | Display | |
Data in XML | ![]() | 366 KB | Display | |
Data in CIF | ![]() | 531.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15865MC ![]() 8b6gC ![]() 8b6hC ![]() 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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Components
+Protein , 36 types, 36 molecules A0A1A2A3A4A5A7A8AFAGAJANASAYAZB1B2B6BABCBEBFBGBIBJBKBNBPBRBS...
-Transmembrane protein, ... , 11 types, 11 molecules A6A9B0B3B4B5BBBDBLBMBX
#7: Protein | Mass: 29389.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#10: Protein | Mass: 26545.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#37: Protein | Mass: 11451.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#40: Protein | Mass: 9942.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#41: Protein | Mass: 8787.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#42: Protein | Mass: 8445.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#45: Protein | Mass: 24419.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#47: Protein | Mass: 23971.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#55: Protein | Mass: 16909.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#56: Protein | Mass: 15831.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#67: Protein | Mass: 13340.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-NADH dehydrogenase subunit ... , 5 types, 5 molecules AAAEAOATBH
#11: 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) |
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#15: 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) |
#25: Protein | Mass: 23830.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q950Z3, NADH:ubiquinone reductase (H+-translocating) |
#30: 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) |
#51: 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) |
-NADH-ubiquinone oxidoreductase ... , 7 types, 7 molecules ABACAHAIALAUAX
#12: Protein | Mass: 80580.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#13: 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) |
#18: 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) |
#19: Protein | Mass: 31216.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#22: Protein | Mass: 28053.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#31: Protein | Mass: 17381.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#34: 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) |
-NADH dehydrogenase [ubiquinone] ... , 6 types, 6 molecules ADAPAQARBOBQ
#14: 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) |
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#26: Protein | Mass: 22890.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#27: Protein | Mass: 22698.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#28: Protein | Mass: 21642.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#58: Protein | Mass: 15689.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#60: Protein | Mass: 15193.583 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Gamma-carbonic ... , 2 types, 2 molecules AKAM
#21: Protein | Mass: 28216.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#23: Protein | Mass: 25395.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Acyl carrier ... , 2 types, 2 molecules AVAW
#32: Protein | Mass: 16249.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#33: Protein | Mass: 15428.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 13 types, 77 molecules ![](data/chem/img/CDL.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/LPP.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/LPP.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/8Q1.gif)
![](data/chem/img/ZN.gif)
#70: Chemical | ChemComp-CDL / #71: Chemical | ChemComp-UDP / | #72: Chemical | #73: Chemical | ChemComp-PC1 / #74: Chemical | ChemComp-NDP / | #75: Chemical | ChemComp-3PE / #76: Chemical | ChemComp-LPP / #77: Chemical | #78: Chemical | #79: Chemical | ChemComp-SF4 / #80: Chemical | ChemComp-FMN / | #81: Chemical | ChemComp-8Q1 / | #82: Chemical | ChemComp-ZN / | |
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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: NADH:ubiquinone oxidoreductase complex (complex-I) from respiratory supercomplex of Tetrahymena thermophila Type: COMPLEX / Entity ID: #1-#69 / Source: NATURAL |
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Molecular weight | Value: 1.52 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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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138746 / Symmetry type: POINT | ||||||||||||||||||||||||
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