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- PDB-9rf1: Structure of human GPX4-U46C-R152K mutant -

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Basic information

Entry
Database: PDB / ID: 9rf1
TitleStructure of human GPX4-U46C-R152K mutant
ComponentsPhospholipid hydroperoxide glutathione peroxidase GPX4
KeywordsSTRUCTURAL PROTEIN / Ferroptosis / GPX4 / Xray
Function / homology
Function and homology information


phospholipid-hydroperoxide glutathione peroxidase / phospholipid-hydroperoxide glutathione peroxidase activity / Synthesis of 12-eicosatetraenoic acid derivatives / Synthesis of 15-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 12-eicosatetraenoic acid derivatives / Synthesis of 15-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 / dendrite development / protein polymerization / phospholipid metabolic process / cerebellum development / multicellular organism growth / nuclear envelope / response to estradiol / chromatin organization / response to oxidative stress / spermatogenesis / response to lipopolysaccharide / apoptotic process / 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: 1.9 Å
AuthorsMourao, A. / Sattler, M. / Popowicz, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Crystal structure of human GPX4-U46C-R152K
Authors: Mourao, A. / Sattler, M. / Popowicz, G.
History
DepositionJun 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipid hydroperoxide glutathione peroxidase GPX4
B: Phospholipid hydroperoxide glutathione peroxidase GPX4


Theoretical massNumber of molelcules
Total (without water)39,2132
Polymers39,2132
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-1 kcal/mol
Surface area16000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.392, 62.952, 75.442
Angle α, β, γ (deg.)90.000, 100.791, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Phospholipid hydroperoxide glutathione peroxidase GPX4 / PHGPx / Glutathione peroxidase 4 / GPx-4 / GSHPx-4


Mass: 19606.635 Da / Num. of mol.: 2 / Mutation: U46C R152K
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, glutathione peroxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium acetate 0.1M BIS-Tris ph 5.5 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 9, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.9→37 Å / Num. obs: 88991 / % possible obs: 98.66 % / Redundancy: 3.5 % / CC1/2: 0.917 / Net I/σ(I): 3.19
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 2547 / CC1/2: 0.316

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→37 Å / SU ML: 0.3468 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2837 1352 5.33 %
Rwork0.2152 24023 -
obs0.2187 25375 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 0 228 2886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672727
X-RAY DIFFRACTIONf_angle_d0.82593678
X-RAY DIFFRACTIONf_chiral_restr0.0584376
X-RAY DIFFRACTIONf_plane_restr0.0057478
X-RAY DIFFRACTIONf_dihedral_angle_d15.4072994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.35621700.32612306X-RAY DIFFRACTION95.97
1.97-2.050.38611400.30032354X-RAY DIFFRACTION98.93
2.05-2.140.30551300.27472404X-RAY DIFFRACTION98.98
2.14-2.250.28621200.25342421X-RAY DIFFRACTION99.18
2.25-2.40.31371240.24192399X-RAY DIFFRACTION98.71
2.4-2.580.31620.22762366X-RAY DIFFRACTION98.48
2.58-2.840.30641230.23212396X-RAY DIFFRACTION98.48
2.84-3.250.28131300.20572443X-RAY DIFFRACTION99.42
3.25-4.090.27321100.16952461X-RAY DIFFRACTION99.5
4.1-370.21821430.17612473X-RAY DIFFRACTION98.98

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