+Open data
-Basic information
Entry | Database: PDB / ID: 8jsc | ||||||
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Title | Structure of the FSP1 protein from Human | ||||||
Components | Ferroptosis suppressor protein 1 | ||||||
Keywords | OXIDOREDUCTASE / NADH-ubiquinone oxidoreductase / OXIDOREDUCTASE (E.C.1.-.-.-) | ||||||
Function / homology | Function and homology information electron-transferring-flavoprotein dehydrogenase activity / ubiquinone metabolic process / negative regulation of ferroptosis / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / vitamin K metabolic process / regulation of cellular response to oxidative stress / cellular detoxification / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release ...electron-transferring-flavoprotein dehydrogenase activity / ubiquinone metabolic process / negative regulation of ferroptosis / Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor / vitamin K metabolic process / regulation of cellular response to oxidative stress / cellular detoxification / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / lipid droplet / flavin adenine dinucleotide binding / mitochondrial outer membrane / positive regulation of apoptotic process / mitochondrion / DNA binding / extracellular space / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Zhang, S.T. / Jia, D. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Res. / Year: 2023 Title: FSP1 oxidizes NADPH to suppress ferroptosis. Authors: Zhang, S. / Gou, S. / Zhang, Q. / Yong, X. / Gan, B. / Jia, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jsc.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jsc.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 8jsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/8jsc ftp://data.pdbj.org/pub/pdb/validation_reports/js/8jsc | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40442.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIFM2, AMID, PRG3 / Production host: Escherichia coli (E. coli) References: UniProt: Q9BRQ8, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor |
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#2: Chemical | ChemComp-6FA / |
#3: Chemical | ChemComp-NAP / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.68 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium nitrate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→62.25 Å / Num. obs: 18472 / % possible obs: 99.4 % / Redundancy: 3.6 % / CC1/2: 0.972 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.16→2.27 Å / Num. unique obs: 2689 / CC1/2: 0.556 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→39.5 Å / SU ML: 0.2844 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9055 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: 18.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.16→39.5 Å
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Refine LS restraints |
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LS refinement shell |
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