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- PDB-8ec0: III2IV respiratory supercomplex from Saccharomyces cerevisiae car... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ec0 | |||||||||
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Title | III2IV respiratory supercomplex from Saccharomyces cerevisiae cardiolipin-lacking mutant | |||||||||
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![]() | OXIDOREDUCTASE / S.cerevisiae / respiratory supercomplex / phosphatidylglycerol | |||||||||
Function / homology | ![]() matrix side of mitochondrial inner membrane / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / mitochondrial respiratory chain complex IV / mitochondrial respiratory chain complex III / cytochrome-c oxidase ...matrix side of mitochondrial inner membrane / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / mitochondrial respiratory chain complex IV / mitochondrial respiratory chain complex III / cytochrome-c oxidase / mitochondrial respirasome / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport / aerobic respiration / nuclear periphery / mitochondrial membrane / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Hryc, C.F. / Mileykovskaya, E. / Baker, M. / Dowhan, W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into cardiolipin replacement by phosphatidylglycerol in a cardiolipin-lacking yeast respiratory supercomplex. Authors: Corey F Hryc / Venkata K P S Mallampalli / Evgeniy I Bovshik / Stavros Azinas / Guizhen Fan / Irina I Serysheva / Genevieve C Sparagna / Matthew L Baker / Eugenia Mileykovskaya / William Dowhan / ![]() Abstract: Cardiolipin is a hallmark phospholipid of mitochondrial membranes. Despite established significance of cardiolipin in supporting respiratory supercomplex organization, a mechanistic understanding of ...Cardiolipin is a hallmark phospholipid of mitochondrial membranes. Despite established significance of cardiolipin in supporting respiratory supercomplex organization, a mechanistic understanding of this lipid-protein interaction is still lacking. To address the essential role of cardiolipin in supercomplex organization, we report cryo-EM structures of a wild type supercomplex (IVIIIIV) and a supercomplex (IIIIV) isolated from a cardiolipin-lacking Saccharomyces cerevisiae mutant at 3.2-Å and 3.3-Å resolution, respectively, and demonstrate that phosphatidylglycerol in IIIIV occupies similar positions as cardiolipin in IVIIIIV. Lipid-protein interactions within these complexes differ, which conceivably underlies the reduced level of IVIIIIV and high levels of IIIIV and free III and IV in mutant mitochondria. Here we show that anionic phospholipids interact with positive amino acids and appear to nucleate a phospholipid domain at the interface between the individual complexes, which dampen charge repulsion and further stabilize interaction, respectively, between individual complexes. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 1023.3 KB | Display | ![]() |
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PDB format | ![]() | 848.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 159.6 KB | Display | |
Data in CIF | ![]() | 236.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 28011MC ![]() 8e7sC 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 b-c1 complex subunit ... , 7 types, 14 molecules AaBbCcEeFfGgHh
#1: Protein | Mass: 50282.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 40528.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 23393.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 7485.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 14583.755 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 17276.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 10987.511 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 2 types, 4 molecules JjLl
#8: Protein | Mass: 43686.590 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 34097.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Cytochrome c oxidase subunit ... , 12 types, 12 molecules KMNOPQRSTUVW
#9: Protein | Mass: 58832.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#11: Protein | Mass: 8921.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 6942.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 30383.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 28585.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 17366.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 6974.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 15046.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 17164.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#19: Protein | Mass: 9799.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#20: Protein | Mass: 7461.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#21: Protein | Mass: 17161.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 9 types, 41 molecules ![](data/chem/img/PEF.gif)
![](data/chem/img/PGT.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PCF.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/UQ6.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/PGT.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/PCF.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/UQ6.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/CUA.gif)
#22: Chemical | ChemComp-PEF / #23: Chemical | ChemComp-PGT / ( #24: Chemical | #25: Chemical | ChemComp-PCF / #26: Chemical | ChemComp-HEM / #27: Chemical | #28: Chemical | ChemComp-CU / | #29: Chemical | #30: 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: III2-IV mitochondrial respiratory supercomplex / Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.2 |
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 magnification: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 49 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 20253 |
Image scans | Width: 360 / Height: 360 / Movie frames/image: 35 / Used frames/image: 1-35 |
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Processing
Software | Name: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1510025 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 745670 / Algorithm: FOURIER SPACE / Symmetry type: POINT |