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Open data
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Basic information
Entry | Database: PDB / ID: 8gs8 | ||||||||||||
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Title | cryo-EM structure of the human respiratory complex II | ||||||||||||
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![]() | OXIDOREDUCTASE / succinate dehydrogenase / electron transport chain / human mitochondria / oxidative phosphorylation | ||||||||||||
Function / homology | ![]() regulation of catecholamine secretion / succinate metabolic process / succinate dehydrogenase activity / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / Citric acid cycle (TCA cycle) / Respiratory electron transport / mitochondrial envelope ...regulation of catecholamine secretion / succinate metabolic process / succinate dehydrogenase activity / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / Citric acid cycle (TCA cycle) / Respiratory electron transport / mitochondrial envelope / anaerobic respiration / 3 iron, 4 sulfur cluster binding / proton motive force-driven mitochondrial ATP synthesis / ubiquinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / nervous system development / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / cellular response to hypoxia / mitochondrial inner membrane / electron transfer activity / heme binding / nucleolus / mitochondrion / nucleoplasm / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å | ||||||||||||
![]() | Du, Z. / Zhou, X. / Lai, Y. / Xu, J. / Zhang, Y. / Zhou, S. / Liu, F. / Gao, Y. / Gong, H. / Rao, Z. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the human respiratory complex II. Authors: Zhanqiang Du / Xiaoting Zhou / Yuezheng Lai / Jinxu Xu / Yuying Zhang / Shan Zhou / Ziyan Feng / Long Yu / Yanting Tang / Weiwei Wang / Lu Yu / Changlin Tian / Ting Ran / Hongming Chen / ...Authors: Zhanqiang Du / Xiaoting Zhou / Yuezheng Lai / Jinxu Xu / Yuying Zhang / Shan Zhou / Ziyan Feng / Long Yu / Yanting Tang / Weiwei Wang / Lu Yu / Changlin Tian / Ting Ran / Hongming Chen / Luke W Guddat / Fengjiang Liu / Yan Gao / Zihe Rao / Hongri Gong / ![]() ![]() Abstract: Human complex II is a key protein complex that links two essential energy-producing processes: the tricarboxylic acid cycle and oxidative phosphorylation. Deficiencies due to mutagenesis have been ...Human complex II is a key protein complex that links two essential energy-producing processes: the tricarboxylic acid cycle and oxidative phosphorylation. Deficiencies due to mutagenesis have been shown to cause mitochondrial disease and some types of cancers. However, the structure of this complex is yet to be resolved, hindering a comprehensive understanding of the functional aspects of this molecular machine. Here, we have determined the structure of human complex II in the presence of ubiquinone at 2.86 Å resolution by cryoelectron microscopy, showing it comprises two water-soluble subunits, SDHA and SDHB, and two membrane-spanning subunits, SDHC and SDHD. This structure allows us to propose a route for electron transfer. In addition, clinically relevant mutations are mapped onto the structure. This mapping provides a molecular understanding to explain why these variants have the potential to produce disease. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 212.7 KB | Display | ![]() |
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PDB format | ![]() | 163 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 46.4 KB | Display | |
Data in CIF | ![]() | 67.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34225MC 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
-Succinate dehydrogenase [ubiquinone] ... , 3 types, 3 molecules ABD
#1: Protein | Mass: 72786.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 31674.811 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Protein | Mass: 17063.990 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 18632.213 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 7 types, 7 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/UQ1.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/PEV.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/UQ1.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/PEV.gif)
#5: Chemical | ChemComp-FAD / |
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#6: Chemical | ChemComp-FES / |
#7: Chemical | ChemComp-SF4 / |
#8: Chemical | ChemComp-F3S / |
#9: Chemical | ChemComp-UQ1 / |
#10: Chemical | ChemComp-HEM / |
#11: Chemical | ChemComp-PEV / ( |
-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: The human mitochondrial complex II, composed of SDHA, SDHB, SDHC and SDHD Type: COMPLEX / Entity ID: #1, #4, #3, #2 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 |
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: 2000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114967 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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