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- PDB-8udc: Crystal structure of TcPINK1 in complex with CYC116 -

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Basic information

Entry
Database: PDB / ID: 8udc
TitleCrystal structure of TcPINK1 in complex with CYC116
ComponentsSerine/threonine-protein kinase Pink1, mitochondrial
KeywordsCELL CYCLE / Mitophagy Autophagy Kinase
Function / homology
Function and homology information


positive regulation of free ubiquitin chain polymerization / positive regulation of mitochondrial fission / positive regulation of protein ubiquitination / autophagy / peptidyl-serine phosphorylation / regulation of apoptotic process / mitochondrial inner membrane / mitochondrial outer membrane / protein autophosphorylation / non-specific serine/threonine protein kinase ...positive regulation of free ubiquitin chain polymerization / positive regulation of mitochondrial fission / positive regulation of protein ubiquitination / autophagy / peptidyl-serine phosphorylation / regulation of apoptotic process / mitochondrial inner membrane / mitochondrial outer membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ubiquitin protein ligase binding / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / : / Serine/threonine-protein kinase Pink1, mitochondrial
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsVeyron, S. / Rasool, S. / Trempe, J.F.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)153274 Canada
Michael J. Fox Foundation12119 United States
CitationJournal: To Be Published
Title: Structural Characterization of a small-molecule inhibitor of PINK1, a precursor tool compound for the study of Parkinson's disease
Authors: Shomali, T. / Rasool, S. / Croteau, N. / Veyron, S. / Truong, L. / Trempe, J.F.
History
DepositionSep 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase Pink1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4694
Polymers50,8981
Non-polymers5713
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.021, 53.021, 546.158
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Serine/threonine-protein kinase Pink1, mitochondrial


Mass: 50898.117 Da / Num. of mol.: 1 / Mutation: W131A,W142A,Y144A,I147A,Y225A,Y378A,F401A,F437A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: Pink1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D6WMX4
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-WCK / (4P)-4-(2-amino-4-methyl-1,3-thiazol-5-yl)-N-[4-(morpholin-4-yl)phenyl]pyrimidin-2-amine


Mass: 368.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 90 mM HEPES 7.0, 17.5% PEG 4K, 0.13 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.1→45.92 Å / Num. obs: 9497 / % possible obs: 100 % / Redundancy: 35.3 % / Biso Wilson estimate: 73.06 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.85 / Net I/σ(I): 7.8
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 38.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1611 / CC1/2: 0.532 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→45.92 Å / SU ML: 0.5104 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.6405
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3293 452 4.83 %
Rwork0.2551 8899 -
obs0.2585 9351 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.06 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 38 15 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01683121
X-RAY DIFFRACTIONf_angle_d1.5584257
X-RAY DIFFRACTIONf_chiral_restr0.0647490
X-RAY DIFFRACTIONf_plane_restr0.0161546
X-RAY DIFFRACTIONf_dihedral_angle_d15.23351114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.550.4531710.33022819X-RAY DIFFRACTION99.9
3.55-4.470.31861310.24852894X-RAY DIFFRACTION99.83
4.47-45.920.28621500.23593186X-RAY DIFFRACTION99.94

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