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- PDB-7mp9: Crystal structure of the cytosolic domain of Tribolium castaneum ... -

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Basic information

Entry
Database: PDB / ID: 7mp9
TitleCrystal structure of the cytosolic domain of Tribolium castaneum PINK1 phosphorylated at Ser205 in complex with ADP analog
ComponentsSerine/threonine-protein kinase PINK1, mitochondrial-like Protein
KeywordsSIGNALING PROTEIN / Kinase / transphorylation
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 outer membrane / protein autophosphorylation / mitochondrial inner membrane / 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 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
AMP PHOSPHORAMIDATE / Serine/threonine-protein kinase Pink1, mitochondrial
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRasool, S. / Veyron, S. / Trempe, J.F.
Funding support Canada, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)153274 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)06497-2015 Canada
Michael J. Fox Foundation12119 Canada
CitationJournal: Mol.Cell / Year: 2022
Title: Mechanism of PINK1 activation by autophosphorylation and insights into assembly on the TOM complex.
Authors: Rasool, S. / Veyron, S. / Soya, N. / Eldeeb, M.A. / Lukacs, G.L. / Fon, E.A. / Trempe, J.F.
History
DepositionMay 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Oct 18, 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

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PINK1, mitochondrial-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,68610
Polymers51,2681
Non-polymers1,4179
Water1,08160
1
A: Serine/threonine-protein kinase PINK1, mitochondrial-like Protein
hetero molecules

A: Serine/threonine-protein kinase PINK1, mitochondrial-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,37220
Polymers102,5372
Non-polymers2,83518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area9780 Å2
ΔGint-143 kcal/mol
Surface area34390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.736, 52.736, 547.944
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
Components on special symmetry positions
IDModelComponents
11A-746-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine/threonine-protein kinase PINK1, mitochondrial-like Protein


Mass: 51268.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: TcasGA2_TC013202 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D6WMX4

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Non-polymers , 5 types, 69 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-AN2 / AMP PHOSPHORAMIDATE


Mass: 426.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N6O9P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / Details: 80mM MES (pH 6.5), 0.16M (NH4)2 SO4, 16% PEG 8K.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→45.67 Å / Num. obs: 9568 / % possible obs: 93.4 % / Redundancy: 34.9 % / Biso Wilson estimate: 33.79 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.6
Reflection shellResolution: 2.8→2.92 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 478 / CC1/2: 0.841 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YJ9

5yj9


Resolution: 2.8→45.67 Å / SU ML: 0.2046 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7183
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3065 444 4.64 %
Rwork0.2469 9121 -
obs0.2497 9565 76.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.38 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 87 60 3335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263337
X-RAY DIFFRACTIONf_angle_d0.54794543
X-RAY DIFFRACTIONf_chiral_restr0.039515
X-RAY DIFFRACTIONf_plane_restr0.0045572
X-RAY DIFFRACTIONf_dihedral_angle_d21.2348484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.20.417640.32421476X-RAY DIFFRACTION38.98
3.2-4.030.33481690.24733430X-RAY DIFFRACTION88.04
4.03-45.670.27272110.23244215X-RAY DIFFRACTION99.95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.7337768062-0.6363506969932.117773939931.65709832354-0.9496801195812.737967717730.218920884058-0.0548049623834-0.19481700316-0.200649889763-0.05218113814610.2575599374410.240221311678-0.160332092611-0.1200603800110.1354511965950.04097604732380.0655539929360.0602925544875-0.04198206836990.097936192606-30.97830586863.67614412426-19.633937291
24.05006197329-0.361301185295-0.4491483474620.21744184491-0.5856758084082.204782102280.03792913163540.695655372634-0.7973807335-0.1365918470080.01464372596660.0978948371620.504366053356-0.2301489285490.2035917641570.1945658653590.0315546573748-0.02783487199660.094918019152-0.1063619038260.177790737381-29.7575460533.42118796843-37.5715139599
31.011048544470.2272515421920.3649110491421.18905520882-0.263272657961.014814256460.1104473949540.1524925368810.141563268922-0.0469883983466-0.07076459113610.0823755166454-0.304465271372-0.02363201384210.02221377072580.07480095248530.08597536323880.0171341345622-0.03575822220910.113490437837-0.0699831035223-18.795828774118.0189956059-27.9734094938
41.25182793346-0.3368823528170.2866103457231.72416112385-0.2225811312051.686470121680.0118082818346-0.251246873303-0.0400644422390.341031001278-0.0320190829707-0.16374792085-0.1329152983130.1196147008530.009693236596140.1398729916820.07185929880980.01055859996210.0884128157488-0.0066040752150.0290236088133-13.722999653215.5647688825-8.75638762237
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 121 through 192 )121 - 1921 - 69
22chain 'A' and (resid 193 through 288 )193 - 28870 - 138
33chain 'A' and (resid 289 through 442 )289 - 442139 - 291
44chain 'A' and (resid 443 through 568 )443 - 568292 - 414

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