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- PDB-9ycu: Protiated human DJ-1, 100K -

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Basic information

Entry
Database: PDB / ID: 9ycu
TitleProtiated human DJ-1, 100K
ComponentsProtein deglycase DJ-1
KeywordsHYDROLASE / PARK7 / glyoxalase / cyclic phosphoglycerate anhydride hydrolase
Function / homology
Function and homology information


positive regulation of acute inflammatory response to antigenic stimulus / tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / guanine deglycation, glyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization ...positive regulation of acute inflammatory response to antigenic stimulus / tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / guanine deglycation, glyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly / negative regulation of TRAIL-activated apoptotic signaling pathway / positive regulation of L-dopa biosynthetic process / glyoxalase (glycolic acid-forming) activity / negative regulation of protein K48-linked deubiquitination / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / glycolate biosynthetic process / detection of oxidative stress / glyoxal metabolic process / guanine deglycation / methylglyoxal metabolic process / detoxification of mercury ion / ubiquitin-protein transferase inhibitor activity / protein deglycase / mercury ion binding / protein deglycase activity / hydrogen peroxide metabolic process / positive regulation of dopamine biosynthetic process / positive regulation of autophagy of mitochondrion / superoxide dismutase copper chaperone activity / oxidoreductase activity, acting on peroxide as acceptor / positive regulation of mitochondrial electron transport, NADH to ubiquinone / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / lactate biosynthetic process / protein repair / peptidase inhibitor activity / cellular detoxification of aldehyde / peroxiredoxin activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / small protein activating enzyme binding / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / detoxification of copper ion / negative regulation of protein sumoylation / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein export from nucleus / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cupric ion binding / regulation of androgen receptor signaling pathway / membrane hyperpolarization / oxygen sensor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / insulin secretion / ubiquitin-like protein conjugating enzyme binding / nuclear androgen receptor binding / androgen receptor signaling pathway / ubiquitin-specific protease binding / dopamine uptake involved in synaptic transmission / cytokine binding / positive regulation of reactive oxygen species biosynthetic process / cuprous ion binding / signaling receptor activator activity / membrane depolarization / regulation of synaptic vesicle endocytosis / single fertilization / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / removal of superoxide radicals / SUMOylation of transcription cofactors / adult locomotory behavior / regulation of mitochondrial membrane potential / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / mitochondrion organization / adherens junction / positive regulation of protein-containing complex assembly / enzyme activator activity / Late endosomal microautophagy / PML body / mitochondrial intermembrane space / autophagy / positive regulation of protein localization to nucleus / kinase binding / cellular response to hydrogen peroxide / Chaperone Mediated Autophagy / positive regulation of reactive oxygen species metabolic process / Aggrephagy / synaptic vesicle / glucose homeostasis / peptidase activity / cell body / cellular response to oxidative stress / response to oxidative stress / regulation of inflammatory response / scaffold protein binding / DNA-binding transcription factor binding
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / : / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsLin, J. / Kovalevsky, A. / Walker, A.R. / Wilson, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM153337 United States
Citation
Journal: To Be Published
Title: Environmental contributions to proton sharing in protein low barrier hydrogen bonds
Authors: Lin, J. / Gerlits, O. / Kneller, D.W. / Weiss, K.L. / Coates, L. / Hix, M.A. / Effah, S.Y. / Kovalevsky, A. / Walker, A.R. / Wilson, M.A.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionSep 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5106
Polymers20,1991
Non-polymers3105
Water5,386299
1
A: Protein deglycase DJ-1
hetero molecules

A: Protein deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,01912
Polymers40,3992
Non-polymers62110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_553x-y,-y,-z-4/31
Buried area4390 Å2
ΔGint8 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.109, 75.109, 75.505
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Protein deglycase DJ-1 / DJ-1 / Oncogene DJ1 / Parkinson disease protein 7


Mass: 20199.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q99497, Hydrolases; Acting on ester bonds; Thioester hydrolases, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22-24% PEG 3000, 200 mM NaCl, and 100 mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.729 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.729 Å / Relative weight: 1
ReflectionResolution: 1.05→37.75 Å / Num. obs: 114819 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 13.18 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.075 / Net I/σ(I): 13.2
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 5635 / CC1/2: 0.252 / Rrim(I) all: 3.838 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→37.55 Å / SU ML: 0.1116 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.4534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1342 3467 3.04 %
Rwork0.1182 110710 -
obs0.1187 114177 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.86 Å2
Refinement stepCycle: LAST / Resolution: 1.05→37.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 20 299 1717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781649
X-RAY DIFFRACTIONf_angle_d1.0832249
X-RAY DIFFRACTIONf_chiral_restr0.0875257
X-RAY DIFFRACTIONf_plane_restr0.0107300
X-RAY DIFFRACTIONf_dihedral_angle_d12.8297673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.060.33721080.33894020X-RAY DIFFRACTION90.59
1.06-1.080.33761250.32054335X-RAY DIFFRACTION98.26
1.08-1.10.291300.2884408X-RAY DIFFRACTION99.58
1.1-1.110.26791270.2584388X-RAY DIFFRACTION99.8
1.11-1.130.22291370.22714436X-RAY DIFFRACTION99.87
1.13-1.150.23171320.21914388X-RAY DIFFRACTION100
1.15-1.170.22481320.19974436X-RAY DIFFRACTION99.91
1.17-1.190.20111370.18724447X-RAY DIFFRACTION100
1.19-1.220.21171480.17044362X-RAY DIFFRACTION100
1.22-1.240.16211660.15574404X-RAY DIFFRACTION100
1.24-1.270.16411320.14484431X-RAY DIFFRACTION99.98
1.27-1.310.15881490.13484396X-RAY DIFFRACTION99.98
1.31-1.340.14311430.12444465X-RAY DIFFRACTION100
1.34-1.380.14051380.11344416X-RAY DIFFRACTION100
1.38-1.430.13271530.09824391X-RAY DIFFRACTION99.98
1.43-1.480.09911520.09044469X-RAY DIFFRACTION100
1.48-1.540.09581270.08034426X-RAY DIFFRACTION100
1.54-1.60.09151570.07794439X-RAY DIFFRACTION100
1.6-1.690.09631450.0764450X-RAY DIFFRACTION100
1.69-1.80.10721290.08224467X-RAY DIFFRACTION100
1.8-1.930.09461300.08244502X-RAY DIFFRACTION100
1.93-2.130.10281510.09414468X-RAY DIFFRACTION99.98
2.13-2.440.09821420.09774501X-RAY DIFFRACTION100
2.44-3.070.12761400.11314542X-RAY DIFFRACTION100
3.07-37.550.15881370.12854723X-RAY DIFFRACTION99.96

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