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- PDB-7owg: human DEPTOR in a complex with mutant human mTORC1 A1459P -

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Basic information

Entry
Database: PDB / ID: 7owg
Titlehuman DEPTOR in a complex with mutant human mTORC1 A1459P
Components
  • DEP domain-containing mTOR-interacting protein
  • Regulatory-associated protein of mTOR
  • Serine/threonine-protein kinase mTOR
  • Target of rapamycin complex subunit LST8
KeywordsSIGNALING PROTEIN / kinase / PIKK / mTOR / cancer-associated mutation / DEPTOR / partial inhibitor / cancer / PDZ / non-canonical PDZ binding
Function / homology
Function and homology information


regulation of extrinsic apoptotic signaling pathway / RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex ...regulation of extrinsic apoptotic signaling pathway / RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability / cellular response to leucine starvation / heart valve morphogenesis / TFIIIC-class transcription factor complex binding / negative regulation of lysosome organization / TORC1 complex / voluntary musculoskeletal movement / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / positive regulation of odontoblast differentiation / calcineurin-NFAT signaling cascade / negative regulation of TORC2 signaling / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of osteoclast differentiation / regulation of lysosome organization / MTOR signalling / cellular response to L-leucine / energy reserve metabolic process / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / cellular response to nutrient / phosphatidic acid binding / Amino acids regulate mTORC1 / TORC1 signaling / cellular response to methionine / serine/threonine protein kinase complex / ruffle organization / negative regulation of cell size / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of osteoclast differentiation / cellular response to osmotic stress / negative regulation of TOR signaling / anoikis / inositol hexakisphosphate binding / negative regulation of protein localization to nucleus / cardiac muscle cell development / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of transcription by RNA polymerase III / negative regulation of macroautophagy / Macroautophagy / positive regulation of myotube differentiation / regulation of cell size / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of actin filament polymerization / protein kinase inhibitor activity / germ cell development / behavioral response to pain / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / TOR signaling / positive regulation of translational initiation / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / social behavior / HSF1-dependent transactivation / positive regulation of G1/S transition of mitotic cell cycle / regulation of macroautophagy / protein serine/threonine kinase inhibitor activity / protein kinase activator activity / positive regulation of TOR signaling / enzyme-substrate adaptor activity / 'de novo' pyrimidine nucleobase biosynthetic process / response to amino acid / positive regulation of epithelial to mesenchymal transition / positive regulation of lipid biosynthetic process / vascular endothelial cell response to laminar fluid shear stress / cellular response to nutrient levels / heart morphogenesis / neuronal action potential / negative regulation of protein kinase activity / regulation of cellular response to heat / positive regulation of lamellipodium assembly / cardiac muscle contraction / positive regulation of stress fiber assembly / T cell costimulation / phagocytic vesicle / 14-3-3 protein binding / positive regulation of endothelial cell proliferation / negative regulation of TORC1 signaling / endomembrane system / cytoskeleton organization / positive regulation of autophagy / negative regulation of insulin receptor signaling pathway / negative regulation of autophagy / GTPase activator activity / cellular response to amino acid starvation / guanyl-nucleotide exchange factor activity / cellular response to starvation / positive regulation of glycolytic process
Similarity search - Function
DEP domain-containing mTOR-interacting protein, DEP domain 1 / DEP domain-containing mTOR-interacting protein, DEP domain 2 / Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / Target of rapamycin complex subunit LST8 / : / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain ...DEP domain-containing mTOR-interacting protein, DEP domain 1 / DEP domain-containing mTOR-interacting protein, DEP domain 2 / Raptor, N-terminal CASPase-like domain / Raptor N-terminal CASPase like domain / Raptor N-terminal CASPase like domain / Regulatory associated protein of TOR / Target of rapamycin complex subunit LST8 / : / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / Serine/threonine-protein kinase ATR-like, HEAT repeats / HEAT repeat / HEAT repeat / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / Armadillo-type fold / Winged helix DNA-binding domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase mTOR / Regulatory-associated protein of mTOR / DEP domain-containing mTOR-interacting protein / Target of rapamycin complex subunit LST8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsHeimhalt, M. / Berndt, A. / Wagstaff, J. / Anandapadamanaban, M. / Perisic, O. / Maslen, S. / McLaughlin, S. / Yu, W.-H. / Masson, G.R. / Boland, A. ...Heimhalt, M. / Berndt, A. / Wagstaff, J. / Anandapadamanaban, M. / Perisic, O. / Maslen, S. / McLaughlin, S. / Yu, W.-H. / Masson, G.R. / Boland, A. / Ni, X. / Yamashita, K. / Murshudov, G.N. / Skehel, M. / Freund, S.M. / Williams, R.L.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105184308 United Kingdom
Cancer Research UKC14801/A21211 United Kingdom
European Molecular Biology Organization (EMBO)EMBO ALTF 603-2019 United Kingdom
CitationJournal: Elife / Year: 2021
Title: Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace.
Authors: Maren Heimhalt / Alex Berndt / Jane Wagstaff / Madhanagopal Anandapadamanaban / Olga Perisic / Sarah Maslen / Stephen McLaughlin / Conny Wing-Heng Yu / Glenn R Masson / Andreas Boland / ...Authors: Maren Heimhalt / Alex Berndt / Jane Wagstaff / Madhanagopal Anandapadamanaban / Olga Perisic / Sarah Maslen / Stephen McLaughlin / Conny Wing-Heng Yu / Glenn R Masson / Andreas Boland / Xiaodan Ni / Keitaro Yamashita / Garib N Murshudov / Mark Skehel / Stefan M Freund / Roger L Williams /
Abstract: The mTORC1 kinase complex regulates cell growth, proliferation, and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted ...The mTORC1 kinase complex regulates cell growth, proliferation, and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted mTORC1 with DEPTOR to understand its function. We find that DEPTOR is a unique mTORC1 inhibitor that may have evolved to preserve feedback inhibition of PI3K. Counterintuitively, mTORC1 activated by RHEB or oncogenic mutation is much more potently inhibited by DEPTOR. Although DEPTOR partially inhibits mTORC1, mTORC1 prevents this inhibition by phosphorylating DEPTOR, a mutual antagonism that requires no exogenous factors. Structural analyses of the mTORC1/DEPTOR complex showed DEPTOR's PDZ domain interacting with the mTOR FAT region, and the unstructured linker preceding the PDZ binding to the mTOR FRB domain. The linker and PDZ form the minimal inhibitory unit, but the N-terminal tandem DEP domains also significantly contribute to inhibition.
History
DepositionJun 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 17, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
B: Serine/threonine-protein kinase mTOR
E: Target of rapamycin complex subunit LST8
O: DEP domain-containing mTOR-interacting protein
Y: Regulatory-associated protein of mTOR


Theoretical massNumber of molelcules
Total (without water)519,0464
Polymers519,0464
Non-polymers00
Water00
1
B: Serine/threonine-protein kinase mTOR
E: Target of rapamycin complex subunit LST8
O: DEP domain-containing mTOR-interacting protein
Y: Regulatory-associated protein of mTOR

B: Serine/threonine-protein kinase mTOR
E: Target of rapamycin complex subunit LST8
O: DEP domain-containing mTOR-interacting protein
Y: Regulatory-associated protein of mTOR


Theoretical massNumber of molelcules
Total (without water)1,038,0938
Polymers1,038,0938
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (-1), (1)303.64417, 303.644172

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Components

#1: Protein Serine/threonine-protein kinase mTOR / FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex- ...FK506-binding protein 12-rapamycin complex-associated protein 1 / FKBP12-rapamycin complex-associated protein / Mammalian target of rapamycin / mTOR / Mechanistic target of rapamycin / Rapamycin and FKBP12 target 1 / Rapamycin target protein 1


Mass: 287570.312 Da / Num. of mol.: 1 / Mutation: A1459P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1, mMTOR / Plasmid: pOPL146 / Details (production host): mTOR in pCAG vector / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
References: UniProt: P42345, non-specific serine/threonine protein kinase
#2: Protein Target of rapamycin complex subunit LST8 / TORC subunit LST8 / G protein beta subunit-like / Protein GbetaL / Mammalian lethal with SEC13 ...TORC subunit LST8 / G protein beta subunit-like / Protein GbetaL / Mammalian lethal with SEC13 protein 8 / mLST8


Mass: 35910.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLST8, GBL, LST8 / Plasmid: pOPL95 / Details (production host): human LST8 cloned in pCAG / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9BVC4
#3: Protein DEP domain-containing mTOR-interacting protein / DEP domain-containing protein 6


Mass: 46365.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEPTOR, DEPDC6 / Plasmid: pOPL138
Details (production host): GST(tev)-Human_DEPTOR_1-409 (S204,N389 natural variant)
Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR / References: UniProt: Q8TB45
#4: Protein Regulatory-associated protein of mTOR / Raptor / p150 target of rapamycin (TOR)-scaffold protein


Mass: 149200.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPTOR, KIAA1303, RAPTOR / Plasmid: pOPL119 / Details (production host): Human_Raptor nontagged, in pCAG / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q8N122

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1COMPLEX OF HUMAN MUTANT MTORC1 A1459P WITH THE INHIBITORY PROTEIN DEPTORCOMPLEXAn mTORC1 complex bound to two copies of DEPTOR. Each mTORC1 complex consists of a dimer of an mTOR/LST8/RAPTOR heterotrimer. The mTOR is an A1459P mutant.all0MULTIPLE SOURCES
2mTORC1 with mutant A1459P mTORCOMPLEXmTORC1 with mutant A1459P mTOR#1-#2, #41RECOMBINANT
3DEPTORCOMPLEXDEPTOR is a natural inhibitor of mTORC1#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.04 MDaNO
210.948 MDaNO
3146.3NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainCellPlasmid
22Homo sapiens (human)9606Expi293FpOPL146, pOPL95 and pOPL119
33Escherichia coli (E. coli)562LOBSTRpOPL138
Buffer solutionpH: 7.5
Details: 50 mM HEPES, pH 7.5, 200 mM NaCl, 1 mM TCEP, 1 mM MgCl2, 500 uM AMP-PNP
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Purified mutant mTORC1 A1459P and DEPTOR were preincubated in the presence of MgCl2 and AMP-PNP for 20 min and used for cryo-EM grid preparation.
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 287 K / Details: blotting time of 2 s and a force of -15.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: -3000 nm / Nominal defocus min: -1400 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 100 K
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 4759
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 6000 / Height: 4000

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Processing

SoftwareName: REFMAC / Version: 5.8.0272 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk / Date: Feb 9, 2020
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Coot0.9model fitting
8ISOLDE1.1model fitting
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
14REFMAC5.8.0272model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 376784
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 500000 / Symmetry type: POINT
Atomic model buildingB value: 145.7 / Protocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: Correlation
Atomic model buildingPDB-ID: 6BCX

6bcx


Pdb chain-ID: B / Accession code: 6BCX / Pdb chain residue range: 1-2549 / Source name: PDB / Type: experimental model
RefinementResolution: 4.7→299.244 Å / Cor.coef. Fo:Fc: 0.974 / WRfactor Rwork: 0.342 / SU B: 108.861 / SU ML: 1.072 / Average fsc overall: 0.7062 / Average fsc work: 0.7062 / ESU R: 0.804
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3418 228193 -
all0.342 --
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 122.054 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.01329148
ELECTRON MICROSCOPYr_bond_other_d0.0320.01727983
ELECTRON MICROSCOPYr_ext_dist_refined_d0.1990.1485563
ELECTRON MICROSCOPYr_angle_refined_deg1.761.63339548
ELECTRON MICROSCOPYr_angle_other_deg1.341.57564184
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.74553564
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.67421.7611533
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.551155062
ELECTRON MICROSCOPYr_dihedral_angle_4_deg20.78815215
ELECTRON MICROSCOPYr_chiral_restr0.1050.23812
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0232682
ELECTRON MICROSCOPYr_gen_planes_other0.0030.026792
ELECTRON MICROSCOPYr_nbd_refined0.1990.213910
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1560.249536
ELECTRON MICROSCOPYr_nbtor_refined0.1560.227440
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0860.229284
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.0790.2976
ELECTRON MICROSCOPYr_symmetry_nbd_refined0.1960.226
ELECTRON MICROSCOPYr_nbd_other0.1960.264
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_refined0.2090.212
ELECTRON MICROSCOPYr_mcbond_it4.03113.05714346
ELECTRON MICROSCOPYr_mcbond_other4.03113.05714345
ELECTRON MICROSCOPYr_mcangle_it6.58519.57917880
ELECTRON MICROSCOPYr_mcangle_other6.58519.57917881
ELECTRON MICROSCOPYr_scbond_it3.33413.1514802
ELECTRON MICROSCOPYr_scbond_other3.33413.1514799
ELECTRON MICROSCOPYr_scangle_it5.8719.67821668
ELECTRON MICROSCOPYr_scangle_other5.8719.67821667
ELECTRON MICROSCOPYr_lrange_it13.191488.114485601
ELECTRON MICROSCOPYr_lrange_other13.191488.112485594
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
4.7-4.8220.49168040.49168040.5530.49
4.822-4.9540.478164060.478164060.5940.478
4.954-5.0980.466160220.466160220.6280.466
5.098-5.2550.452155610.452155610.6580.452
5.255-5.4270.443150710.443150710.6590.443
5.427-5.6170.446145870.446145870.660.446
5.617-5.8290.444140200.444140200.660.444
5.829-6.0670.455136670.455136670.6640.455
6.067-6.3370.461129260.461129260.6740.461
6.337-6.6460.451124470.451124470.7010.451
6.646-7.0050.438117770.438117770.7260.438
7.005-7.430.433110870.433110870.7420.433
7.43-7.9430.399105660.399105660.7710.399
7.943-8.5790.37796990.37796990.7950.377
8.579-9.3970.34889860.34889860.8370.348
9.397-10.5040.31381020.31381020.8830.313
10.504-12.1270.27671890.27671890.9120.276
12.127-14.8460.24560470.24560470.9340.245
14.846-20.970.21646410.21646410.9460.216
20.97-299.2440.12325880.12325880.9910.123

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