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- PDB-5h5s: Crystal structure of human GPX4 in complex with GXpep-3 -

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Basic information

Entry
Database: PDB / ID: 5h5s
TitleCrystal structure of human GPX4 in complex with GXpep-3
Components
  • GXpep-3
  • Phospholipid hydroperoxide glutathione peroxidase, mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE 4 / SELENOCYSTEINE / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phospholipid hydroperoxide glutathione peroxidase GPX4
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSogabe, S. / Kadotani, A. / Lane, W. / Snell, G.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Discovery of GPX4 inhibitory peptides from random peptide T7 phage display and subsequent structural analysis
Authors: Sakamoto, K. / Sogabe, S. / Kamada, Y. / Matsumoto, S.I. / Kadotani, A. / Sakamoto, J.I. / Tani, A.
History
DepositionNov 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipid hydroperoxide glutathione peroxidase, mitochondrial
B: GXpep-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0573
Polymers20,9652
Non-polymers921
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-7 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.017, 39.077, 59.394
Angle α, β, γ (deg.)90.00, 97.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19403.070 Da / Num. of mol.: 1 / Mutation: 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
#2: Protein/peptide GXpep-3


Mass: 1561.887 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T7 (virus)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 1.92 Å3/Da / Density % sol: 35.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M MES pH 5.5, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 13498 / % possible obs: 97.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.1
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 1.8 / % possible all: 76.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OBI

2obi


Resolution: 1.85→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.569 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.136 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20383 670 5 %RANDOM
Rwork0.1663 ---
obs0.16816 12817 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.791 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.3 Å2
2---0.43 Å2-0 Å2
3---0.89 Å2
Refinement stepCycle: 1 / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 6 126 1573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191492
X-RAY DIFFRACTIONr_bond_other_d0.0020.021415
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.952017
X-RAY DIFFRACTIONr_angle_other_deg0.95833263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7235178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46224.22571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.65315255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.667157
X-RAY DIFFRACTIONr_chiral_restr0.0870.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211678
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02355
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_it0.3911.075712
X-RAY DIFFRACTIONr_mcbond_other0.3911.075711
X-RAY DIFFRACTIONr_mcangle_it0.6981.607887
X-RAY DIFFRACTIONr_mcangle_other0.6981.608888
X-RAY DIFFRACTIONr_scbond_it0.4191.148780
X-RAY DIFFRACTIONr_scbond_other0.4181.148780
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7181.6991130
X-RAY DIFFRACTIONr_long_range_B_refined3.79313.7521771
X-RAY DIFFRACTIONr_long_range_B_other3.52513.081726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 44 -
Rwork0.25 703 -
obs--76.07 %
Refinement TLS params.Method: refined / Origin x: 6.6973 Å / Origin y: 0.1968 Å / Origin z: 14.354 Å
111213212223313233
T0.0055 Å20.004 Å2-0.0005 Å2-0.0223 Å20.008 Å2--0.0079 Å2
L1.0059 °20.0936 °20.5192 °2-1.2319 °20.0397 °2--1.3968 °2
S0.0048 Å °0.088 Å °0.0007 Å °-0.0264 Å °0.0255 Å °0.0735 Å °0.049 Å °0.0073 Å °-0.0302 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 197
2X-RAY DIFFRACTION1B901 - 914

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