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Open data
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Basic information
Entry | Database: PDB / ID: 8ues | ||||||
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Title | In-situ complex I, Deactive class01 | ||||||
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![]() | ELECTRON TRANSPORT / in-situ cryo-EM structure / mammalian / mitochondria / respiratory supercomplex / proton pumping / membrane protein | ||||||
Function / homology | ![]() RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / Mitochondrial protein degradation / cardiac muscle tissue development / ubiquinone-6 biosynthetic process / cellular respiration / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity ...RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / Mitochondrial protein degradation / cardiac muscle tissue development / ubiquinone-6 biosynthetic process / cellular respiration / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial ATP synthesis coupled electron transport / : / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / acyl binding / ubiquinone binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / quinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / response to cAMP / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / electron transport chain / regulation of protein phosphorylation / brain development / mitochondrial intermembrane space / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / NAD binding / positive regulation of fibroblast proliferation / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / nuclear body / mitochondrial matrix / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
![]() | Zheng, W. / Zhu, J. / Zhang, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: High-resolution in situ structures of mammalian respiratory supercomplexes. Authors: Wan Zheng / Pengxin Chai / Jiapeng Zhu / Kai Zhang / ![]() ![]() Abstract: Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in ...Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: IIIIIV, IIIIIV, IIIIIV and IIIIIV, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.7 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 | ![]() 42169MC ![]() 8ud1C ![]() 8ueoC ![]() 8uepC ![]() 8ueqC ![]() 8uerC ![]() 8uetC ![]() 8ueuC ![]() 8uevC ![]() 8uewC ![]() 8uexC ![]() 8ueyC ![]() 8uezC ![]() 8ugdC ![]() 8ugeC ![]() 8ugfC ![]() 8uggC ![]() 8ughC ![]() 8ugiC ![]() 8ugjC ![]() 8ugkC ![]() 8uglC ![]() 8ugnC ![]() 8ugpC ![]() 8ugrC 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
-NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules 1A1H1J1K1L1M1N
#1: Protein | Mass: 13026.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O79880, NADH:ubiquinone reductase (H+-translocating) |
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#8: Protein | Mass: 35619.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: A0A0U1RS44, NADH:ubiquinone reductase (H+-translocating) |
#10: Protein | Mass: 19049.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O79882, NADH:ubiquinone reductase (H+-translocating) |
#11: Protein | Mass: 10855.263 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P56632, NADH:ubiquinone reductase (H+-translocating) |
#12: Protein | Mass: 68723.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q9TDR1, NADH:ubiquinone reductase (H+-translocating) |
#13: Protein | Mass: 51887.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O79881, NADH:ubiquinone reductase (H+-translocating) |
#14: Protein | Mass: 39105.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: O79875, NADH:ubiquinone reductase (H+-translocating) |
-NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules 1B1C1D1I1Q1R1e
#2: Protein | Mass: 28500.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Protein | Mass: 30154.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 54168.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 27135.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 19746.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 13348.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#30: Protein | Mass: 12506.591 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules 1E1F1s
#5: Protein | Mass: 27439.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#6: Protein | Mass: 50637.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#44: Protein | Mass: 48217.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 1 types, 1 molecules 1G
#7: Protein | Mass: 79627.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 10 types, 10 molecules 1O1S1V1W1X1Y1a1b1q1r
#15: Protein | Mass: 40476.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#19: Protein | Mass: 11099.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#21: Protein | Mass: 13321.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#22: Protein | Mass: 14953.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#23: Protein | Mass: 20064.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#24: Protein | Mass: 14686.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#26: Protein | Mass: 8034.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#27: Protein | Mass: 9225.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#42: Protein | Mass: 17162.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#43: Protein | Mass: 12674.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH:ubiquinone oxidoreductase subunit ... , 4 types, 5 molecules 1P1T1U1Z1j
#16: Protein | Mass: 42606.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
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#20: Protein | Mass: 17338.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #25: Protein | | Mass: 16911.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #35: Protein | | Mass: 11939.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules 1c1d
#28: Protein | Mass: 8664.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#29: Protein | Mass: 14353.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 10 types, 10 molecules 1f1g1h1i1k1l1m1n1o1p
#31: Protein | Mass: 15371.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#32: Protein | Mass: 17384.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#33: Protein | Mass: 21587.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#34: Protein | Mass: 15645.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#36: Protein | Mass: 11128.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#37: Protein | Mass: 21658.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#38: Protein | Mass: 15117.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#39: Protein | Mass: 21864.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#40: Protein | Mass: 16487.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#41: Protein | Mass: 20944.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 14 types, 31 molecules ![](data/chem/img/3PE.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EHZ.gif)
![](data/chem/img/PGT.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/CDL.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/EHZ.gif)
![](data/chem/img/PGT.gif)
![](data/chem/img/MYR.gif)
#45: Chemical | ChemComp-3PE / #46: Chemical | ChemComp-SF4 / #47: Chemical | #48: Chemical | ChemComp-FMN / | #49: Chemical | ChemComp-K / | #50: Chemical | ChemComp-PC1 / #51: Chemical | #52: Chemical | ChemComp-GTP / | #53: Chemical | ChemComp-MG / | #54: Chemical | ChemComp-NDP / | #55: Chemical | ChemComp-ZN / | #56: Chemical | #57: Chemical | ChemComp-PGT / ( | #58: Chemical | ChemComp-MYR / | |
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-Details
Has ligand of interest | N |
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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: In-situ cryo-EM structure of respiratory supercomplex by directly imaging mitochondria Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#44 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7 |
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: 3000 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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