[English] 日本語
Yorodumi
- PDB-5h5q: Crystal structure of human GPX4 in complex with GXpep-1 -

+
Open data


ID or keywords:

Loading...

-
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 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. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more