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- PDB-8ugr: In-situ structure of typeX supercomplex in respiratory chain (com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ugr | ||||||
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Title | In-situ structure of typeX supercomplex in respiratory chain (composite) | ||||||
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![]() | ELECTRON TRANSPORT / in-situ cryo-EM structure / mammalian / mitochondria / respiratory supercomplex / proton pumping / membrane protein | ||||||
Function / homology | ![]() Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / RHOG GTPase cycle / respiratory chain complex IV / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / mitochondrial respiratory chain complex IV ...Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / mitochondrial respirasome assembly / RHOG GTPase cycle / respiratory chain complex IV / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / mitochondrial respiratory chain complex IV / regulation of oxidative phosphorylation / Mitochondrial protein degradation / mitochondrial respiratory chain complex III / deoxynucleoside kinase activity / cytochrome-c oxidase / cardiac muscle tissue development / mitochondrial respirasome / quinol-cytochrome-c reductase / ubiquinone-6 biosynthetic process / ubiquinol-cytochrome-c reductase activity / oxidoreductase activity, acting on NAD(P)H / mitochondrial electron transport, cytochrome c to oxygen / cellular respiration / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I / mitochondrial electron transport, NADH to ubiquinone / ubiquinone binding / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / electron transport coupled proton transport / quinone binding / ATP synthesis coupled electron transport / enzyme regulator activity / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vasoconstriction / response to cAMP / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / central nervous system development / electron transport chain / regulation of protein phosphorylation / brain development / mitochondrial intermembrane space / negative regulation of cell growth / metalloendopeptidase activity / 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 / electron transfer activity / oxidoreductase activity / nuclear body / mitochondrial matrix / copper ion binding / heme binding / protein-containing complex binding / mitochondrion / proteolysis / nucleoplasm / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å | ||||||
![]() | Zheng, W. / Zhang, K. / Zhu, J. | ||||||
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 | ![]() | 5.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 7.4 MB | Display | ![]() |
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Full document | ![]() | 7.8 MB | Display | |
Data in XML | ![]() | 697.1 KB | Display | |
Data in CIF | ![]() | 1 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 42233MC ![]() 8ud1C ![]() 8ueoC ![]() 8uepC ![]() 8ueqC ![]() 8uerC ![]() 8uesC ![]() 8uetC ![]() 8ueuC ![]() 8uevC ![]() 8uewC ![]() 8uexC ![]() 8ueyC ![]() 8uezC ![]() 8ugdC ![]() 8ugeC ![]() 8ugfC ![]() 8uggC ![]() 8ughC ![]() 8ugiC ![]() 8ugjC ![]() 8ugkC ![]() 8uglC ![]() 8ugnC ![]() 8ugpC 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
+NADH-ubiquinone oxidoreductase chain ... , 7 types, 14 molecules 1A5A1H5H1J5J1K5K1L5L1M5M1N5N
+NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 14 molecules 1B5B1C5C1D5D1I5I1Q5Q1R5R1e5e
+NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 6 molecules 1E5E1F5F1s5s
+Protein , 4 types, 14 molecules 1G5G3C3P6C6P3D3Q6D6Q3J3W6J6W
+NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 10 types, 20 molecules 1O5O1S5S1V5V1W5W1X5X1Y5Y1a5a1b5b1q5q1r5r
+NADH:ubiquinone oxidoreductase subunit ... , 4 types, 10 molecules 1P5P1T1U5T5U1Z5Z1j5j
+NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 4 molecules 1c5c1d5d
+NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 10 types, 20 molecules 1f5f1g5g1h5h1i5i1k5k1l5l1m5m1n5n1o5o1p5p
+Cytochrome b-c1 complex subunit ... , 7 types, 32 molecules 3A3N6A6N3B3O6B6O3E3I3R3V6E6I6R6V3F3S6F6S3G3T6G6T3H3U6H6U3X3Y6X6Y
+Cytochrome c oxidase subunit ... , 14 types, 28 molecules 4A8A4B8B4C8C4D8D4E8E4F8F4G8G4H8H4I8I4J8J4K8K4L8L4M8M4N8N
+Non-polymers , 25 types, 190 molecules ![](data/chem/img/3PE.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/K.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/AME.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/AYA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/PSC.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PC1.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/K.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/AME.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/AYA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/HEA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CUA.gif)
![](data/chem/img/PSC.gif)
![](data/chem/img/PEK.gif)
![](data/chem/img/PO4.gif)
+Details
-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: COMPLEX / Entity ID: #1-#39, #41-#68 / 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: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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