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- PDB-8uct: Crystal structure of TcPINK1 in complex with PRT -

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Basic information

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


positive regulation of free ubiquitin chain polymerization / autophagy of mitochondrion / positive regulation of mitochondrial fission / positive regulation of protein ubiquitination / peptidyl-serine phosphorylation / regulation of apoptotic process / mitochondrial outer membrane / protein autophosphorylation / mitochondrial inner membrane / non-specific serine/threonine protein kinase ...positive regulation of free ubiquitin chain polymerization / autophagy of mitochondrion / positive regulation of mitochondrial fission / positive regulation of protein ubiquitination / peptidyl-serine phosphorylation / regulation of apoptotic process / mitochondrial outer membrane / protein autophosphorylation / mitochondrial inner membrane / 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
Chem-3YT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Serine/threonine-protein kinase Pink1, mitochondrial
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 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: Characterization of a new family of PINK1 inhibitors
Authors: Shomali, T. / Rasool, S. / Croteau, N. / Veyron, S. / Truong, L. / Trempe, J.F.
History
DepositionSep 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 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)51,7725
Polymers51,0321
Non-polymers7404
Water41423
1
A: Serine/threonine-protein kinase Pink1, mitochondrial
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)103,54410
Polymers102,0652
Non-polymers1,4808
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5140 Å2
ΔGint-91 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.216, 53.216, 545.580
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: 51032.293 Da / Num. of mol.: 1 / Mutation: W131A, W142A, 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-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-3YT / 2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-{[3-(2H-1,2,3-triazol-2-yl)phenyl]amino}pyrimidine-5-carboxamide


Mass: 393.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N9O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 43.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100mM HEPES, PEG 4000, 150mM 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: 0.987 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.93→90.93 Å / Num. obs: 11014 / % possible obs: 100 % / Redundancy: 17.8 % / Biso Wilson estimate: 75.42 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.145 / Net I/σ(I): 6.1
Reflection shellResolution: 2.93→2.98 Å / Redundancy: 16.9 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 521 / CC1/2: 0.551 / % 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: 2.93→90.93 Å / SU ML: 0.4527 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3052 546 5.04 %
Rwork0.2834 10293 -
obs0.2845 10839 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.82 Å2
Refinement stepCycle: LAST / Resolution: 2.93→90.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 47 23 3051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663092
X-RAY DIFFRACTIONf_angle_d0.77614217
X-RAY DIFFRACTIONf_chiral_restr0.0423489
X-RAY DIFFRACTIONf_plane_restr0.0126547
X-RAY DIFFRACTIONf_dihedral_angle_d16.61971123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-3.230.37251150.39192308X-RAY DIFFRACTION93.48
3.23-3.70.39021430.33832535X-RAY DIFFRACTION99.93
3.7-4.660.2831240.25592612X-RAY DIFFRACTION99.93
4.66-90.930.2781640.25772838X-RAY DIFFRACTION99.97

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