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Yorodumi- PDB-8dyd: Crystal structure of human SDHA-SDHAF2-SDHAF4 assembly intermediate -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dyd | ||||||||||||
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Title | Crystal structure of human SDHA-SDHAF2-SDHAF4 assembly intermediate | ||||||||||||
Components |
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Keywords | FLAVOPROTEIN / SDHA / SDHAF2 / SDHAF4 / ASSEMBLY INTERMEDIATE / RESPIRATORY COMPLEX / OXIDOREDUCTASE / ELECTRON TRANSPORT | ||||||||||||
Function / homology | Function and homology information protein-FAD linkage / mitochondrial respiratory chain complex II assembly / succinate metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase ...protein-FAD linkage / mitochondrial respiratory chain complex II assembly / succinate metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of TCA cycle / Respiratory electron transport / negative regulation of epithelial to mesenchymal transition / cellular respiration / proton motive force-driven mitochondrial ATP synthesis / tricarboxylic acid cycle / enzyme activator activity / protein folding chaperone / protein dephosphorylation / respiratory electron transport chain / negative regulation of canonical Wnt signaling pathway / flavin adenine dinucleotide binding / nervous system development / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / innate immune response / nucleolus / mitochondrion / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||||||||
Authors | Sharma, P. / Maklashina, E. / Cecchini, G. / Iverson, T.M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dyd.cif.gz | 492.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dyd.ent.gz | 386.4 KB | Display | PDB format |
PDBx/mmJSON format | 8dyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dyd_validation.pdf.gz | 783.1 KB | Display | wwPDB validaton report |
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Full document | 8dyd_full_validation.pdf.gz | 792.9 KB | Display | |
Data in XML | 8dyd_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 8dyd_validation.cif.gz | 53.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/8dyd ftp://data.pdbj.org/pub/pdb/validation_reports/dy/8dyd | HTTPS FTP |
-Related structure data
Related structure data | 8dyeC 3sfdS 6vaxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 69416.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SDHA, SDH2, SDHF / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P31040, succinate dehydrogenase |
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-Succinate dehydrogenase assembly factor ... , 2 types, 2 molecules BC
#2: Protein | Mass: 16592.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SDHAF2, C11orf79, PGL2, SDH5 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9NX18 |
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#3: Protein | Mass: 11227.444 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SDHAF4, C6orf57 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5VUM1 |
-Non-polymers , 7 types, 556 molecules
#4: Chemical | ChemComp-FAD / | ||||||||||
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#5: Chemical | #6: Chemical | ChemComp-K / | #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-EDO / #9: Chemical | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 200 mM Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→50 Å / Num. obs: 122221 / % possible obs: 91.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 16.73 Å2 / CC1/2: 0.904 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.041 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.52→1.57 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 11699 / CC1/2: 0.648 / Rpim(I) all: 0.491 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VAX, 3SFD Resolution: 1.52→35.49 Å / SU ML: 0.1489 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.312 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: 24.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→35.49 Å
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Refine LS restraints |
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LS refinement shell |
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