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- PDB-7l8m: Crystal structure of human GPX4-U46C mutant K48L -

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Basic information

Entry
Database: PDB / ID: 7l8m
TitleCrystal structure of human GPX4-U46C mutant K48L
ComponentsPhospholipid hydroperoxide glutathione peroxidase
KeywordsOXIDOREDUCTASE / 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 / negative regulation of ferroptosis / selenium binding / glutathione peroxidase / Synthesis of 5-eicosatetraenoic acids / lipoxygenase pathway / arachidonic acid metabolic process ...phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 15-eicosatetraenoic acid derivatives / Synthesis of 12-eicosatetraenoic acid derivatives / negative regulation of ferroptosis / selenium binding / glutathione peroxidase / Synthesis of 5-eicosatetraenoic acids / lipoxygenase pathway / arachidonic acid metabolic process / Biosynthesis of aspirin-triggered D-series resolvins / Biosynthesis of E-series 18(R)-resolvins / Biosynthesis of D-series resolvins / Biosynthesis of E-series 18(S)-resolvins / glutathione peroxidase activity / long-chain fatty acid biosynthetic process / protein polymerization / phospholipid metabolic process / response to estradiol / nuclear envelope / chromatin organization / cellular response to oxidative stress / spermatogenesis / response to oxidative stress / protein-containing complex / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Thioredoxin-like superfamily
Similarity search - Domain/homology
Phospholipid hydroperoxide glutathione peroxidase GPX4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsForouhar, F. / Liu, H. / Seibt, T. / Saneto, R. / Friedman, J. / Xia, X. / Shchepinov, M.S. / Ramesh, S. / Conrad, M. / Stockwell, B.R.
Funding support United States, Germany, Russian Federation, European Union, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R61NS109407 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA87497 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA209896 United States
Marie Sklodowska-Curie Actions, FragNET ITN03VP04260 Germany
Ministry of Science and Higher Education of the Russian Federation075-15-2019-1933 Russian Federation
European Research Council (ERC)GA 884754European Union
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM141256 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM124165 United States
CitationJournal: 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
DepositionDec 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipid hydroperoxide glutathione peroxidase


Theoretical massNumber of molelcules
Total (without water)21,8721
Polymers21,8721
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.751, 69.838, 35.789
Angle α, β, γ (deg.)90.000, 116.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phospholipid hydroperoxide glutathione peroxidase / PHGPx / Glutathione peroxidase 4 / GSHPx-4


Mass: 21872.076 Da / Num. of mol.: 1 / Mutation: U46C,K48A
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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.68 Å3/Da / Density % sol: 26.76 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6
Details: 0.1 M sodium chloride, 0.1 M MES, 40% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.07→69.8 Å / Num. obs: 8738 / % possible obs: 96.5 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 5.8
Reflection shellResolution: 2.07→2.2 Å / Num. unique obs: 1261 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L8K

7l8k


Resolution: 2.07→34.92 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 889 10.18 %
Rwork0.1701 7843 -
obs0.1766 8732 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.67 Å2 / Biso mean: 34.1753 Å2 / Biso min: 15.99 Å2
Refinement stepCycle: final / Resolution: 2.07→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 0 60 1388
Biso mean---38.09 -
Num. residues----165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.20.33991660.25091261142798
2.2-2.370.29841530.23941297145098
2.37-2.610.27161260.18611335146199
2.61-2.980.2471690.17381281145098
2.99-3.760.22461290.14861329145899
3.76-34.920.18831460.14661340148698
Refinement TLS params.Method: refined / Origin x: 0.4023 Å / Origin y: 0.0731 Å / Origin z: 13.0986 Å
111213212223313233
T0.1852 Å2-0.0005 Å2-0.0003 Å2-0.1976 Å20.0011 Å2--0.2034 Å2
L0.4843 °2-0.2382 °2-0.0132 °2-0.4395 °2-0.2399 °2--0.3536 °2
S0.0088 Å °0.0984 Å °-0.0935 Å °-0.0427 Å °0.0316 Å °-0.0018 Å °-0.0147 Å °0.0096 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 170
2X-RAY DIFFRACTION1allS1 - 60

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