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- PDB-7l8q: Crystal structure of human GPX4-U46C with oxidized Cys-46 -

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Basic information

Entry
Database: PDB / ID: 7l8q
TitleCrystal structure of human GPX4-U46C with oxidized Cys-46
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
ACETATE ION / Phospholipid hydroperoxide glutathione peroxidase GPX4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsForouhar, 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
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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipid hydroperoxide glutathione peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0543
Polymers21,9361
Non-polymers1182
Water3,819212
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)32.757, 69.035, 35.678
Angle α, β, γ (deg.)90.000, 115.880, 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: 21936.096 Da / Num. of mol.: 1 / Mutation: C46 is oxidized to sulfone
Source method: isolated from a genetically manipulated source
Details: Cys-46 is oxidized, so I named it SFO. / Source: (gene. exp.) Homo sapiens (human) / Gene: GPX4 / Production host: Escherichia coli (E. coli)
References: UniProt: P36969, phospholipid-hydroperoxide glutathione peroxidase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.65 Å3/Da / Density % sol: 25.66 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5
Details: 0.1 M potassium thiocyanate, 0.1 M sodium acetate, and 20% (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-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.48→69.04 Å / Num. obs: 23698 / % possible obs: 99 % / Redundancy: 3.3 % / CC1/2: 0.99 / Net I/σ(I): 16
Reflection shellResolution: 1.48→1.5 Å / Redundancy: 2.8 % / Num. unique obs: 1049 / CC1/2: 0.64 / % possible all: 87.4

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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: 1.48→34.52 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 20.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1821 2346 10.08 %
Rwork0.154 20917 -
obs0.157 23263 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.23 Å2 / Biso mean: 22.5835 Å2 / Biso min: 7.07 Å2
Refinement stepCycle: final / Resolution: 1.48→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 8 212 1553
Biso mean--26.63 35.49 -
Num. residues----165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.48-1.510.43661430.4291136127993
1.51-1.540.34711400.32911204134495
1.54-1.580.27821310.25631205133696
1.58-1.620.21251470.19881219136696
1.62-1.660.21321350.16671213134898
1.66-1.710.19761310.15731242137398
1.71-1.770.21571180.15041222134096
1.77-1.830.18871220.15761240136297
1.83-1.90.18431530.14611236138999
1.9-1.990.17531390.15041235137499
1.99-2.090.19371410.15371242138399
2.09-2.230.17231340.14881275140999
2.23-2.40.17851240.14821240136498
2.4-2.640.18381190.15261252137198
2.64-3.020.18521460.160912681414100
3.02-3.80.14761560.12621228138499
3.8-34.520.1571670.13091260142799
Refinement TLS params.Method: refined / Origin x: 0.1821 Å / Origin y: -0.3321 Å / Origin z: 13.1804 Å
111213212223313233
T0.0463 Å2-0.0023 Å20.0006 Å2-0.0502 Å2-0.0134 Å2--0.0423 Å2
L1.6728 °2-0.0193 °2-0.1931 °2-1.0127 °2-0.0348 °2--0.8746 °2
S0.0196 Å °0.0844 Å °-0.0188 Å °0.0127 Å °0.0093 Å °0.01 Å °-0.0044 Å °-0.0002 Å °0.1037 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA6 - 170
2X-RAY DIFFRACTION1allA201 - 202
3X-RAY DIFFRACTION1allS1 - 212

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