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- PDB-8q8n: Crystal structure of human GPX4-U46C-I129S-L130S -

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Basic information

Entry
Database: PDB / ID: 8q8n
TitleCrystal structure of human GPX4-U46C-I129S-L130S
ComponentsPhospholipid hydroperoxide glutathione peroxidase
KeywordsOXIDOREDUCTASE / redox / ferroptosis / gpx4 / membrane associated / metabolism
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 / arachidonate metabolic process / Biosynthesis of aspirin-triggered D-series 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 / arachidonate 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 / 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
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
AuthorsBostock, M.J. / Mourao, A. / Napolitano, V. / Sattler, M. / Conrad, M. / Popowicz, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: An ultra-rare variant of GPX4 reveals the structural basis to avert neurodegeneration
Authors: Lorenz, S.M. / Wahida, A. / Elmer, D. / Bostock, M.J. / Seibt, T. / Mourao, A. / Trumbach, D. / Rizzollo, F. / Napolitano, V. / Kolonko-Adamska, M. / Sommer, J. / Woo, M.S. / Rothammer, N. / ...Authors: Lorenz, S.M. / Wahida, A. / Elmer, D. / Bostock, M.J. / Seibt, T. / Mourao, A. / Trumbach, D. / Rizzollo, F. / Napolitano, V. / Kolonko-Adamska, M. / Sommer, J. / Woo, M.S. / Rothammer, N. / Gaussman, S. / Alves, F. / Burkle, E. / Wanninger, J. / Boxleitner, K.M. / Stadler, M. / Doll, S. / Mishima, E. / Nakamura, T. / Maida, A. / Hass, D. / Escamilla-Ayala, A. / Puentes, L.P. / Lenberg, J. / Friedman, J. / Scale, C. / Proneth, B. / Henkelmann, B. / Aldrovandi, M. / Agostinis, P. / Zimprich, A. / Vogt-Weisenhorn, D. / Holter-Koch, S. / Lewerenz, J. / Steinacker, P. / Garcia-Saez, A.J. / Wurst, W. / Tietze, A. / Mann, M. / Westmeyer, G.G. / Friese, M.A. / Ramesh, S.K. / Wigby, K. / Sattler, M. / Ingold, I. / Ayton, S. / Jayavelu, A.K. / Popowicz, G. / Conrad, M.
History
DepositionAug 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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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)19,5821
Polymers19,5821
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.235, 45.642, 84.514
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19582.488 Da / Num. of mol.: 1
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


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1.83 Å3/Da / Density % sol: 32.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES monohydrate pH 6.0, 6% v/v Tacsimate pH 6.0, 25% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 30, 2020 / Details: Monochromator + Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→45.64 Å / Num. obs: 12301 / % possible obs: 99.8 % / Redundancy: 12.1 % / CC1/2: 0.832 / Net I/σ(I): 9.5
Reflection shellResolution: 1.88→1.92 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 766 / CC1/2: 0.598 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.29 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.85 / SU B: 12.679 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29209 631 5.3 %RANDOM
Rwork0.20201 ---
obs0.20697 11220 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.459 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0 Å2-0 Å2
2---1.62 Å20 Å2
3---2.46 Å2
Refinement stepCycle: 1 / Resolution: 1.9→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 0 78 1394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131381
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171267
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.6361870
X-RAY DIFFRACTIONr_angle_other_deg1.4131.592931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4825172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12923.7572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39615237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.308155
X-RAY DIFFRACTIONr_chiral_restr0.0850.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021605
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02329
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4621.74676
X-RAY DIFFRACTIONr_mcbond_other1.4615.004675
X-RAY DIFFRACTIONr_scbond_it1.9971.212705
X-RAY DIFFRACTIONr_scbond_other1.9962.74705
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5249.2051020
X-RAY DIFFRACTIONr_rigid_bond_restr3.9931360
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 46 -
Rwork0.44 793 -
obs--99.41 %
Refinement TLS params.Method: refined / Origin x: 8.4463 Å / Origin y: 2.2475 Å / Origin z: 10.4554 Å
111213212223313233
T0.0047 Å20.0096 Å20.004 Å2-0.0305 Å20.0174 Å2--0.0256 Å2
L2.9791 °20.4401 °20.2773 °2-2.5448 °20.0848 °2--2.2098 °2
S0.0024 Å °-0.1266 Å °0.0188 Å °-0.0218 Å °0.0291 Å °0.2074 Å °-0.0609 Å °-0.105 Å °-0.0315 Å °

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