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- PDB-6m8z: Crystal structure of human DJ-1 without a modification on Cys-106 -

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Basic information

Entry
Database: PDB / ID: 6m8z
TitleCrystal structure of human DJ-1 without a modification on Cys-106
ComponentsProtein/nucleic acid deglycase DJ-1
KeywordsUNKNOWN FUNCTION / the exact function of this protein is still unknown
Function / homology
Function and homology information


tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / glutathione deglycation / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate ...tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / glutathione deglycation / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal 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 pyrroline-5-carboxylate reductase activity / positive regulation of tyrosine 3-monooxygenase activity / positive regulation of L-dopa biosynthetic process / positive regulation of L-dopa decarboxylase activity / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / glyoxalase (glycolic acid-forming) activity / negative regulation of protein K48-linked deubiquitination / negative regulation of ubiquitin-specific protease activity / protein deglycation, glyoxal removal / glycolate biosynthetic process / guanine deglycation, glyoxal removal / glyoxal metabolic process / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / guanine deglycation / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / oxidoreductase activity, acting on peroxide as acceptor / protein deglycase activity / positive regulation of acute inflammatory response to antigenic stimulus / positive regulation of dopamine biosynthetic process / superoxide dismutase copper chaperone activity / positive regulation of NAD(P)H oxidase activity / positive regulation of autophagy of mitochondrion / lactate biosynthetic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular detoxification of aldehyde / positive regulation of superoxide dismutase activity / small protein activating enzyme binding / Hydrolases; Acting on ester bonds; Thioester hydrolases / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of ubiquitin-protein transferase activity / peroxiredoxin activity / detoxification of copper ion / negative regulation of protein acetylation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of transcription regulatory region DNA binding / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of androgen receptor activity / membrane hyperpolarization / protein deglycosylation / negative regulation of protein sumoylation / oxygen sensor activity / regulation of androgen receptor signaling pathway / negative regulation of protein export from nucleus / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / cupric ion binding / ubiquitin-like protein conjugating enzyme binding / insulin secretion / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / dopamine uptake involved in synaptic transmission / positive regulation of reactive oxygen species biosynthetic process / nuclear androgen receptor binding / hydrogen peroxide metabolic process / ubiquitin-specific protease binding / cytokine binding / cuprous ion binding / single fertilization / membrane depolarization / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / negative regulation of protein ubiquitination / activation of protein kinase B activity / mitochondrion organization / adult locomotory behavior / SUMOylation of transcription cofactors / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / negative regulation of protein binding / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein-containing complex assembly / adherens junction / Late endosomal microautophagy / negative regulation of protein kinase activity / mitochondrial intermembrane space / PML body / cellular response to hydrogen peroxide / autophagy
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.83 Å
AuthorsShumilin, I.A. / Shabalin, I.G. / Shumilina, S.V. / Werenskjold, C. / Utepbergenov, D. / Minor, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: A transient post-translational modification of active site cysteine alters binding properties of the parkinsonism protein DJ-1.
Authors: Mussakhmetov, A. / Shumilin, I.A. / Nugmanova, R. / Shabalin, I.G. / Baizhumanov, T. / Toibazar, D. / Khassenov, B. / Minor, W. / Utepbergenov, D.
History
DepositionAug 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein/nucleic acid deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3193
Polymers20,0451
Non-polymers2742
Water3,207178
1
A: Protein/nucleic acid deglycase DJ-1
hetero molecules

A: Protein/nucleic acid deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6386
Polymers40,0902
Non-polymers5484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+5/61
Buried area3590 Å2
ΔGint-36 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.500, 66.500, 176.728
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-806-

HOH

21A-869-

HOH

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Components

#1: Protein Protein/nucleic acid deglycase DJ-1 / Maillard deglycase / Oncogene DJ1 / Parkinson disease protein 7 / Parkinsonism-associated deglycase ...Maillard deglycase / Oncogene DJ1 / Parkinson disease protein 7 / Parkinsonism-associated deglycase / Protein DJ-1 / DJ-1


Mass: 20045.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Plasmid: pHisParallel / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL
References: UniProt: Q99497, Hydrolases; Acting on ester bonds; Thioester hydrolases, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, protein deglycase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 500 nL of protein in 50 mM Tris pH 8.0 and 500 mM NaCl were mixed with 500nL of 0.1M Bis-tris pH 5.5, 0.1M KSCN, and 29% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 20934 / % possible obs: 97.8 % / Redundancy: 20.2 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.012 / Rrim(I) all: 0.056 / Χ2: 1.087 / Net I/σ(I): 11 / Num. measured all: 423474
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.83-1.8615.81.2488300.5960.3241.2940.80579.3
1.86-1.916.11.0549280.6320.271.0920.79890
1.9-1.9317.70.8210130.8660.1990.8460.82998.3
1.93-1.9720.50.65810280.9350.1470.6740.88898.9
1.97-2.0121.50.53910490.9620.1170.5520.81199.2
2.01-2.0621.40.43810250.9760.0950.4480.85199.2
2.06-2.1121.50.32210350.9840.070.330.90699.2
2.11-2.1721.50.27110450.990.0590.2780.9499.3
2.17-2.2321.30.20710390.9940.0450.2120.96199.5
2.23-2.3121.40.17810540.9950.0390.1821.02699.4
2.31-2.3921.30.14710430.9970.0320.1511.07299.5
2.39-2.4821.40.12410520.9970.0270.1271.11799.5
2.48-2.621.20.10310540.9970.0230.1061.299.7
2.6-2.7321.20.08510630.9990.0190.0871.26699.6
2.73-2.9210.06610810.9990.0150.0681.31599.6
2.9-3.1320.90.05610610.9990.0120.0571.43599.6
3.13-3.4420.40.04610850.9990.010.0471.48799.9
3.44-3.94200.04111110.9990.0090.0421.59199.7
3.94-4.9719.60.03411240.9990.0080.0351.36599.5
4.97-5017.80.025121410.0060.0260.80196.4

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6E5Z

6e5z


Resolution: 1.83→32.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.264 / SU ML: 0.08 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.11
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 1051 5.2 %RANDOM
Rwork0.1699 ---
obs0.1718 19231 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.52 Å2 / Biso mean: 29.366 Å2 / Biso min: 7.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å2-0 Å2
2---0.4 Å20 Å2
3---1.29 Å2
Refinement stepCycle: final / Resolution: 1.83→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 8 178 1561
Biso mean--42.35 40.61 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0141408
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171377
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.6561904
X-RAY DIFFRACTIONr_angle_other_deg0.8771.6443226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67623.39356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56715256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.927157
X-RAY DIFFRACTIONr_chiral_restr0.0590.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02219
LS refinement shellResolution: 1.83→1.877 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 50 -
Rwork0.243 920 -
all-970 -
obs--63.69 %
Refinement TLS params.Method: refined / Origin x: 28.435 Å / Origin y: 2.224 Å / Origin z: 67.191 Å
111213212223313233
T0.1867 Å20.1005 Å20.0574 Å2-0.0906 Å20.0317 Å2--0.0656 Å2
L1.3109 °20.2043 °2-0.2471 °2-1.5009 °2-0.3253 °2--3.9134 °2
S-0.084 Å °0.1472 Å °-0.1329 Å °-0.139 Å °-0.1546 Å °-0.2781 Å °0.6317 Å °0.352 Å °0.2386 Å °

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