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- PDB-5h5q: Crystal structure of human GPX4 in complex with GXpep-1 -

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Basic information

Entry
Database: PDB / ID: 5h5q
TitleCrystal structure of human GPX4 in complex with GXpep-1
Components
  • GXpep-1
  • 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: 1.1 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 1.2Nov 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 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: Phospholipid hydroperoxide glutathione peroxidase, mitochondrial
B: GXpep-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3364
Polymers21,1522
Non-polymers1842
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-5 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.746, 72.242, 39.616
Angle α, β, γ (deg.)90.00, 108.41, 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: 19419.070 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-1


Mass: 1733.082 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 0.1M potassium formate, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 65137 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.3
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.2 / % possible all: 81.4

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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: 1.1→37.59 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.89 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18368 3245 5 %RANDOM
Rwork0.16341 ---
obs0.1644 61861 91.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.236 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20.31 Å2
2---0.18 Å2-0 Å2
3---0.25 Å2
Refinement stepCycle: 1 / Resolution: 1.1→37.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 12 140 1614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191538
X-RAY DIFFRACTIONr_bond_other_d0.0030.021459
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9482076
X-RAY DIFFRACTIONr_angle_other_deg1.01833356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.01823.51981
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53115273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4811512
X-RAY DIFFRACTIONr_chiral_restr0.3530.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022435
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02379
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_it0.610.888723
X-RAY DIFFRACTIONr_mcbond_other0.610.885721
X-RAY DIFFRACTIONr_mcangle_it1.0221.33902
X-RAY DIFFRACTIONr_mcangle_other1.0221.33902
X-RAY DIFFRACTIONr_scbond_it0.8871.044815
X-RAY DIFFRACTIONr_scbond_other0.8861.044815
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4381.511170
X-RAY DIFFRACTIONr_long_range_B_refined3.68310.4312235
X-RAY DIFFRACTIONr_long_range_B_other3.5269.7282177
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 180 -
Rwork0.358 3628 -
obs--72.46 %
Refinement TLS params.Method: refined / Origin x: -3.5265 Å / Origin y: 19.2958 Å / Origin z: -14.6153 Å
111213212223313233
T0.0004 Å20.0004 Å2-0.0005 Å2-0.0084 Å2-0.0063 Å2--0.0077 Å2
L0.6861 °2-0.2097 °2-0.0437 °2-0.7584 °2-0.1551 °2--0.4936 °2
S-0.0102 Å °-0.0292 Å °0.005 Å °0.0131 Å °0.0205 Å °-0.0093 Å °0.0044 Å °-0.0221 Å °-0.0102 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 197
2X-RAY DIFFRACTION1B900 - 914

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