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Open data
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Basic information
Entry | Database: PDB / ID: 8dye | |||||||||
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Title | Crystal structure of human SDHA-SDHAF4 assembly intermediate | |||||||||
![]() | (Succinate dehydrogenase ...) x 2 | |||||||||
![]() | FLAVOPROTEIN / SDHA / SDHAF4 / ASSEMBLY INTERMEDIATE / RESPIRATORY COMPLEX / OXIDOREDUCTASE | |||||||||
Function / homology | ![]() mitochondrial respiratory chain complex II assembly / succinate metabolic process / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / Citric acid cycle (TCA cycle) / Respiratory electron transport / cellular respiration / anaerobic respiration ...mitochondrial respiratory chain complex II assembly / succinate metabolic process / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / Citric acid cycle (TCA cycle) / Respiratory electron transport / cellular respiration / anaerobic respiration / proton motive force-driven mitochondrial ATP synthesis / enzyme activator activity / tricarboxylic acid cycle / respiratory electron transport chain / nervous system development / flavin adenine dinucleotide binding / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / innate immune response / nucleolus / mitochondrion Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sharma, P. / Maklashina, E. / Cecchini, G. / Iverson, T.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Disordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners. Authors: Sharma, P. / Maklashina, E. / Voehler, M. / Balintova, S. / Dvorakova, S. / Kraus, M. / Vanova, K.H. / Nahacka, Z. / Zobalova, R. / Boukalova, S. / Cunatova, K. / Mracek, T. / Ghayee, H.K. / ...Authors: Sharma, P. / Maklashina, E. / Voehler, M. / Balintova, S. / Dvorakova, S. / Kraus, M. / Vanova, K.H. / Nahacka, Z. / Zobalova, R. / Boukalova, S. / Cunatova, K. / Mracek, T. / Ghayee, H.K. / Pacak, K. / Rohlena, J. / Neuzil, J. / Cecchini, G. / Iverson, T.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 458.6 KB | Display | ![]() |
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PDB format | ![]() | 310.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 31.2 KB | Display | |
Data in CIF | ![]() | 45.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dydC ![]() 3sfdS ![]() 6vaxS S: Starting model for refinement 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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Unit cell |
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Components
-Succinate dehydrogenase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 67150.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 11227.444 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 6 types, 445 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-FAD / | ||||||
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#4: Chemical | ChemComp-MLI / | ||||||
#5: Chemical | ChemComp-EDO / #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 100 mM Sodium malonate, 12 % w/v PEG 3350, 1 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→50 Å / Num. obs: 125714 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 18.63 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 35.61 |
Reflection shell | Resolution: 1.45→1.48 Å / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 6190 / CC1/2: 0.548 / Rsym value: 1.39 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6VAX, 3SFD Resolution: 1.44→28.57 Å / SU ML: 0.1351 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.2603 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→28.57 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -22.185020435 Å / Origin y: 32.9800611895 Å / Origin z: -17.049469302 Å
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Refinement TLS group | Selection details: all |