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- PDB-7mp8: Crystal structure of the cytosolic domain of Tribolium castaneum ... -

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Basic information

Entry
Database: PDB / ID: 7mp8
TitleCrystal structure of the cytosolic domain of Tribolium castaneum PINK1 in the non-phosphorylated state
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
Serine/threonine-protein kinase Pink1, mitochondrial
Similarity search - Component
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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)51,3013
Polymers51,1081
Non-polymers1922
Water61334
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)102,6016
Polymers102,2172
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area4740 Å2
ΔGint-41 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.914, 52.914, 545.362
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-like Protein


Mass: 51108.387 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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 42.95 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES (pH 7.0), 0.15M (NH4)2 SO4, 20% PEG 4K. Temp = 295K

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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: 3→49.58 Å / Num. obs: 10223 / % possible obs: 100 % / Redundancy: 16.4 % / Biso Wilson estimate: 62.83 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.737 / Net I/σ(I): 6.1
Reflection shellResolution: 3→3.18 Å / Redundancy: 12.6 % / Rmerge(I) obs: 3.613 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1589 / CC1/2: 0.627 / % possible all: 100

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Processing

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

5yj9


Resolution: 3→45.82 Å / SU ML: 0.2757 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9754
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3062 478 4.68 %
Rwork0.2538 9745 -
obs0.2564 10223 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.81 Å2
Refinement stepCycle: LAST / Resolution: 3→45.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 10 34 3058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00443087
X-RAY DIFFRACTIONf_angle_d0.66794217
X-RAY DIFFRACTIONf_chiral_restr0.0412493
X-RAY DIFFRACTIONf_plane_restr0.007542
X-RAY DIFFRACTIONf_dihedral_angle_d21.24061093
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.430.36761360.323109X-RAY DIFFRACTION99.75
3.43-4.330.32091590.25483173X-RAY DIFFRACTION99.76
4.33-45.820.28091830.23033463X-RAY DIFFRACTION99.92
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)
13.61455903532-0.9751381623695.346805035042.26592581631-1.816705517317.946159627040.669309246294-0.109111176586-0.458742909482-0.1990583102320.1234951939320.470190577770.649862289682-0.428730757137-0.8738257937750.9018304010220.023280032681-0.04134466821560.5935798925730.1364100175670.652213459648-20.9425310344-1.225227011-11.5910321496
29.189253891330.6853397844260.9640885443259.56671408475-0.4726578740329.732212238960.1650977084960.883993760540.777903100298-0.602788083258-0.214605093728-0.29856792903-0.400476567558-0.3876277737010.207347347760.3672054509050.02087786783530.06640107078020.401455564088-0.01118526591330.561183828612-45.15387760939.58891629336-28.5098311221
31.511254777450.595668249666-0.6644245578911.899020916480.2132799136622.13734813256-0.1005520020990.652399783845-0.18956707959-0.2162038388160.08731127671950.0427150523048-0.637031105738-0.227871578002-0.09319094753590.6097747664040.1944143593950.01567661603150.8086754139080.0372813662110.563841902535-32.17737415498.28108244645-41.047793026
44.052660868131.671334786442.967577798283.287482889252.52477612428.703123249240.09185880986980.792114028178-0.3939838051380.2084389562460.3414215339140.6700843255251.175330800420.0330413374344-0.5815737564210.70322128531-0.0570472501669-0.02765363239540.6475166099680.1152793695340.604576832928-27.31863395030.248123107977-32.5282134249
53.110455408851.060763604980.4524598643922.145119176921.973955294333.310544498940.1533009596640.1650397006230.133257808725-0.0642945448232-0.357919321350.233860630139-0.0355970931383-0.5192713500480.1810845441920.5118528753140.09134678080690.08517689644830.4703406649590.07338548256360.415314261969-27.485553113514.3348234962-24.92635777
64.029453097080.159605481916-0.7615178133571.947693928212.176258177586.213079540580.05080917152690.5153223354340.606610214724-0.2167168972460.04145057429390.0387347025505-0.459533880995-0.116580843022-0.1037535799540.6003168814630.1322369098440.1069495099160.3874421936590.1610446201070.496084113225-13.113383759221.9557622298-33.4037748283
73.558886629340.1024419842030.633848182874.07822389666-2.27928670075.74875082640.060573905927-0.1911135293640.1981197029180.6508215659170.1113009275940.0592157519716-0.6800073750330.389147735342-0.1410471092930.642560776495-0.002982094716350.06296206849770.437178304138-0.04951916905470.384205518202-10.367833039218.3603756241-10.5707638064
87.74126494069-3.33629212682.539067922494.350880842691.464811931417.46371118369-0.160696976294-0.459585103916-0.425912688930.2923547332940.179288032436-0.2983867963750.5041584859490.202586633636-0.0840626332650.687333126203-0.07458035247330.003133444207840.3543902538070.05948463237230.360870538519-13.075031251812.8966831496-9.28846400842
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 153 )121 - 1531 - 33
22chain 'A' and (resid 154 through 192 )154 - 19234 - 69
33chain 'A' and (resid 193 through 220 )193 - 22070 - 97
44chain 'A' and (resid 221 through 252 )221 - 25298 - 127
55chain 'A' and (resid 253 through 371 )253 - 371128 - 221
66chain 'A' and (resid 372 through 443 )372 - 443222 - 293
77chain 'A' and (resid 444 through 515 )444 - 515294 - 365
88chain 'A' and (resid 516 through 567 )516 - 567366 - 399

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