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- PDB-9k7q: Parkinson disease protein 7 (DJ-1) and Alpha-synuclein (Alpha-syn... -

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Basic information

Entry
Database: PDB / ID: 9k7q
TitleParkinson disease protein 7 (DJ-1) and Alpha-synuclein (Alpha-syn) complex
Components
  • Alpha-synuclein
  • Parkinson disease protein 7
KeywordsPROTEIN BINDING / Parkinson disease protein 7 (DJ-1) / Alpha-synuclein (Alpha-syn)
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 / hydrogen peroxide metabolic process / positive regulation of dopamine biosynthetic process / protein deglycase activity / 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 / lactate biosynthetic process / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / 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 / cupric ion binding / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / regulation of androgen receptor signaling pathway / negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / membrane hyperpolarization / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / regulation of synaptic vesicle recycling / negative regulation of chaperone-mediated autophagy / mitochondrial membrane organization / regulation of reactive oxygen species biosynthetic process / oxygen sensor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of glutamate secretion / insulin secretion / ubiquitin-like protein conjugating enzyme binding / dopamine biosynthetic process / nuclear androgen receptor binding / response to iron(II) ion / SNARE complex assembly / regulation of locomotion / positive regulation of neurotransmitter secretion / negative regulation of dopamine metabolic process / positive regulation of inositol phosphate biosynthetic process / regulation of macrophage activation / regulation of norepinephrine uptake / negative regulation of microtubule polymerization / synaptic vesicle transport / androgen receptor signaling pathway / transporter regulator activity / synaptic vesicle priming / ubiquitin-specific protease binding / cytokine binding / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / mitochondrial ATP synthesis coupled electron transport / regulation of dopamine secretion / positive regulation of reactive oxygen species biosynthetic process / dynein complex binding / negative regulation of thrombin-activated receptor signaling pathway / positive regulation of receptor recycling / cuprous ion binding / nuclear outer membrane / response to magnesium ion
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / : / DJ-1/PfpI / DJ-1/PfpI family / Synuclein / Alpha-synuclein / Synuclein / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
Alpha-synuclein / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.58 Å
AuthorsHan, C.W. / Kim, D.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Parkinson disease protein 7 (DJ-1) and Alpha-synuclein (Alpha-syn) complex
Authors: Han, C.W. / Kim, D.H. / Jang, S.B.
History
DepositionOct 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 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: Parkinson disease protein 7
D: Parkinson disease protein 7
E: Parkinson disease protein 7
F: Parkinson disease protein 7
H: Parkinson disease protein 7
J: Parkinson disease protein 7
M: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)127,1267
Polymers127,1267
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, 300kDa
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.285, 75.274, 75.390
Angle α, β, γ (deg.)89.89, 89.92, 60.04
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 19670.768 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / 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, protein deglycase
#2: Protein Alpha-synuclein / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP


Mass: 9101.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37840
Has protein modificationN

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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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium iodide, 20% w/v Polyethylene glycol 3,350, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.53→50 Å / Num. obs: 5769 / % possible obs: 98.6 % / Redundancy: 3.1 % / CC1/2: 0.96 / Net I/σ(I): 1.2
Reflection shellResolution: 4.53→4.61 Å / Num. unique obs: 7763 / CC1/2: 0.947

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.58→7.66 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.852 / SU B: 73.074 / SU ML: 0.923 / Cross valid method: THROUGHOUT / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22247 326 5.3 %RANDOM
Rwork0.14495 ---
obs0.14866 5769 75.39 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.437 Å2
Baniso -1Baniso -2Baniso -3
1--17.08 Å28.8 Å22.54 Å2
2--23.63 Å2-22.21 Å2
3----6.55 Å2
Refinement stepCycle: 1 / Resolution: 4.58→7.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8885 0 0 0 8885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0129019
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.63112166
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.91851207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.42223.608352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.244151635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8891542
X-RAY DIFFRACTIONr_chiral_restr0.0980.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026497
X-RAY DIFFRACTIONr_gen_planes_other
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_it7.8226.3654849
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it13.4099.5166049
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.2016.2854170
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined25.53637805
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A5833
12D5833
21A5812
22E5812
31A5824
32F5824
41A5841
42H5841
51A5827
52J5827
61D5796
62E5796
71D5829
72F5829
81D5810
82H5810
91D5807
92J5807
101E5818
102F5818
111E5806
112H5806
121E5819
122J5819
131F5830
132H5830
141F5830
142J5830
151H5822
152J5822
LS refinement shellResolution: 4.584→4.702 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.086 18 -
Rwork0.141 419 -
obs--65.91 %

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