+Open data
-Basic information
Entry | Database: PDB / ID: 7l8l | |||||||||||||||||||||||||||
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Title | Crystal structure of human R152H GPX4-U46C | |||||||||||||||||||||||||||
Components | Phospholipid hydroperoxide glutathione peroxidase | |||||||||||||||||||||||||||
Keywords | OXIDOREDUCTASE / alpha-beta protein | |||||||||||||||||||||||||||
Function / homology | Function and homology information phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / selenium binding / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase / lipoxygenase pathway / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins ...phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / selenium binding / Synthesis of 5-eicosatetraenoic acids / glutathione peroxidase / lipoxygenase pathway / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / arachidonate metabolic process / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / glutathione peroxidase activity / long-chain fatty acid biosynthetic process / negative regulation of ferroptosis / protein polymerization / phospholipid metabolic process / response to estradiol / nuclear envelope / chromatin organization / spermatogenesis / response to oxidative stress / protein-containing complex / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | |||||||||||||||||||||||||||
Authors | Forouhar, F. / Liu, H. / Seibt, T. / Saneto, R. / Wigby, K. / Friedman, J. / Xia, X. / Shchepinov, M.S. / Ramesh, S. / Conrad, M. / Stockwell, B.R. | |||||||||||||||||||||||||||
Funding support | United States, Germany, Russian Federation, European Union, 8items
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Citation | Journal: Nat.Chem.Biol. / Year: 2021 Title: Patient-derived variant of GPX4 reveals the structural basis for its catalytic activity and degradation mechanism Authors: Liu, H. / Forouhar, F. / Seibt, T. / Saneto, R. / Wigby, K. / Friedman, J. / Xia, X. / Shchepinov, M.S. / Ramesh, S. / Conrad, M. / Stockwell, B.R. | |||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l8l.cif.gz | 85.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l8l.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 7l8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/7l8l ftp://data.pdbj.org/pub/pdb/validation_reports/l8/7l8l | HTTPS FTP |
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-Related structure data
Related structure data | 7l8kSC 7l8mC 7l8qC 7l8rC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21869.051 Da / Num. of mol.: 1 / Mutation: U46C, R152H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GPX4 / Production host: Escherichia coli (E. coli) References: UniProt: P36969, phospholipid-hydroperoxide glutathione peroxidase |
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#2: Chemical | ChemComp-SCN / |
#3: 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: 1.68 Å3/Da / Density % sol: 26.73 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6.9 Details: 0.2 M sodium thiocyanate, pH 6.9, and 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.61→35.1 Å / Num. obs: 17072 / % possible obs: 92.1 % / Redundancy: 3.3 % / CC1/2: 0.97 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.61→1.65 Å / Num. unique obs: 1158 / CC1/2: 0.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7L8K Resolution: 1.61→35.05 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 21.49 / Stereochemistry target values: ML
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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 max: 104.99 Å2 / Biso mean: 13.9155 Å2 / Biso min: 3.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.61→35.05 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: 0.0691 Å / Origin y: 0.1198 Å / Origin z: 13.0549 Å
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Refinement TLS group |
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