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- PDB-9j6l: Solution structure of human Glutathione Peroxidase 4 (Sec73Cys) w... -

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Basic information

Entry
Database: PDB / ID: 9j6l
TitleSolution structure of human Glutathione Peroxidase 4 (Sec73Cys) with eight mutations
ComponentsPhospholipid hydroperoxide glutathione peroxidase GPX4
KeywordsAPOPTOSIS / ferroptosis / cancer / enzyme / peroxidase
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)
MethodSOLUTION NMR / simulated annealing
AuthorsFuruita, K. / Sugiki, T. / Inomata, K. / Miyanoiri, Y. / Kobayashi, N. / Fujiwara, T. / Kojima, C.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04856 Japan
Japan Society for the Promotion of Science (JSPS)22H05536 Japan
Japan Society for the Promotion of Science (JSPS)20H03191 Japan
Japan Society for the Promotion of Science (JSPS)22K19184 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101072 Japan
CitationJournal: To Be Published
Title: Glutathione Disulfide Acts as a Feedback Inhibitor of GPx4 Redox Reaction through Allosteric Regulation
Authors: Inomata, K. / Furuita, K. / Sugiki, T. / Nakada, K. / Kodama, T.S. / Miyanoiri, Y. / Kobayashi, N. / Fujiwara, T. / Kojima, C.
History
DepositionAug 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 20, 2025Provider: 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 GPX4


Theoretical massNumber of molelcules
Total (without water)19,8521
Polymers19,8521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 19851.635 Da / Num. of mol.: 1
Mutation: T27H, C29S, C37A, C64S, U73C, C93R, C102S, C134E, C175V
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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC aliphatic
132isotropic12D 1H-13C HSQC aromatic
142isotropic12D 1H-1H NOESY
152isotropic13D HNCO
162isotropic13D HN(CA)CO
172isotropic13D CBCA(CO)NH
182isotropic13D HN(CA)CB
192isotropic13D HBHA(CO)NH
1102isotropic13D (H)CCH-TOCSY
1112isotropic13D 1H-13C NOESY aliphatic
1122isotropic13D 1H-13C NOESY aromatic
1132isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution150 mM potassium phosphate, 50 mM potassium chloride, 1 mM DTT, 0.4 mM [U-15N] Phospholipid hydroperoxide glutathione peroxidase GPX4, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
solution250 mM potassium phosphate, 50 mM potassium chloride, 1 mM DTT, 0.4 mM [U-13C; U-15N] Phospholipid hydroperoxide glutathione peroxidase GPX4, 95% H2O/5% D2O13C15N_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMpotassium phosphatenatural abundance1
50 mMpotassium chloridenatural abundance1
1 mMDTTnatural abundance1
0.4 mMPhospholipid hydroperoxide glutathione peroxidase GPX4[U-15N]1
50 mMpotassium phosphatenatural abundance2
50 mMpotassium chloridenatural abundance2
1 mMDTTnatural abundance2
0.4 mMPhospholipid hydroperoxide glutathione peroxidase GPX4[U-13C; U-15N]2
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
hmsISTHyberts SG, Wagner Gprocessing
MagRO-NMRViewKobayashi, N.peak picking
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
MagRO-NMRViewKobayashi, N.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
Amber20Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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