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- PDB-6u06: Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking -

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Basic information

Entry
Database: PDB / ID: 6u06
TitleDiscovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking
ComponentsEukaryotic translation initiation factor 4E
KeywordsTRANSLATION / cap-binding site / anti-neoplastic / inhibitor / translation initiation blocking / TRANSLATION-INHIBITOR complex
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / chromatoid body / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / RISC complex / nuclear export / postsynaptic cytosol / stem cell population maintenance / behavioral fear response / negative regulation of neuron differentiation / mRNA export from nucleus / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / translational initiation / P-body / neuron differentiation / cytoplasmic stress granule / G1/S transition of mitotic cell cycle / regulation of translation / DNA-binding transcription factor binding / postsynapse / negative regulation of translation / nuclear body / nuclear speck / translation / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EI8 / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsWan, X.B. / Shoichet, B.K. / Taunton, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35 GM122481 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking.
Authors: Wan, X. / Yang, T. / Cuesta, A. / Pang, X. / Balius, T.E. / Irwin, J.J. / Shoichet, B.K. / Taunton, J.
History
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 11, 2020Group: 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
Revision 1.3Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4E
C: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5718
Polymers88,5804
Non-polymers1,9904
Water2,810156
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6432
Polymers22,1451
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6432
Polymers22,1451
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6432
Polymers22,1451
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6432
Polymers22,1451
Non-polymers4981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.110, 38.290, 146.820
Angle α, β, γ (deg.)87.960, 94.870, 101.640
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Eukaryotic translation initiation factor 4E / mRNA cap-binding protein / eIF-4F 25 kDa subunit


Mass: 22145.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: covalent lysine inhibitor / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eif4e / Production host: Escherichia coli (E. coli) / References: UniProt: P63073
#2: Chemical
ChemComp-EI8 / 3-{[(4-cyanophenyl)methyl](1-oxo-1,2-dihydroisoquinolin-7-yl)sulfamoyl}benzene-1-sulfonyl fluoride


Mass: 497.519 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H16FN3O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.2 / Details: HEPES, MPD, PEG 6K, NDSB-256

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11685 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11685 Å / Relative weight: 1
ReflectionResolution: 1.78→146.21 Å / Num. obs: 55811 / % possible obs: 95.89 % / Redundancy: 2.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.51
Reflection shellResolution: 1.78→1.86 Å / Num. unique obs: 5583 / CC1/2: 0.467

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Processing

Software
NameVersionClassification
PHENIXphenix-1.13-2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DT6

4dt6


Resolution: 1.96→73.132 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.42
RfactorNum. reflection% reflection
Rfree0.2394 2721 4.88 %
Rwork0.1972 --
obs0.1994 55775 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.65 Å2 / Biso mean: 53.4701 Å2 / Biso min: 16.19 Å2
Refinement stepCycle: final / Resolution: 1.96→73.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5929 0 132 156 6217
Biso mean--70.73 41.73 -
Num. residues----728
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)Rfactor Rfree error
1.96-1.99560.30171290.2669282295
1.9956-2.0340.3081330.25462770960
2.034-2.07560.32891190.25682764960
2.0756-2.12070.29331580.24682820940
2.1207-2.170.28881270.24742774970
2.17-2.22430.29141290.2282791940
2.2243-2.28440.26291650.21912770960
2.2844-2.35170.24611400.21632769960
2.3517-2.42760.28981320.21372769950
2.4276-2.51430.24141370.20932810960
2.5143-2.6150.24831370.21692771960
2.615-2.7340.27981630.21782826960
2.734-2.87820.30041250.21382828980
2.8782-3.05850.25851570.20662778960
3.0585-3.29470.24411730.20642766960
3.2947-3.62620.23611310.19192816970
3.6262-4.15090.22361540.17072824960
4.1509-5.22950.20781460.15862729950
5.2295-73.1320.19571660.18072857980
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)
14.0488-0.19141.25313.4057-1.1697.32550.4631-0.3962-0.331-0.1852-0.4273-0.04461.03180.1849-0.00250.21210.1423-0.05440.4284-0.01350.416914.2314-22.0894-7.6744
20.7999-0.86210.12732.6271-0.68041.5107-0.2668-0.17030.7390.27670.3494-0.2029-0.43560.3599-0.0020.2518-0.0528-0.02610.1741-0.01710.5651-0.30793.472-14.5752
30.4355-1.18340.36385.3943-2.60791.5786-0.4768-0.11261.1078-0.1658-0.04220.6516-0.6892-0.13430.06210.4366-0.0147-0.30370.3001-0.06210.85964.2351.3854-13.726
42.09150.59130.82542.1381-0.58522.60990.0015-0.36290.38020.1597-0.0954-0.1334-0.1953-0.17510.10250.1707-0.0042-0.03330.244-0.01930.2441-0.9787-9.0281-10.6601
53.7131-0.291.95322.647-1.17465.7662-0.26170.73590.7574-0.5770.3308-0.1249-0.93660.76050.14690.3394-0.154-0.04260.39950.10140.42998.8279-1.0662-26.3133
61.45920.23950.83171.6786-0.39832.0162-0.18920.11260.1386-0.25080.1250.22070.0816-0.37280.02430.2023-0.0451-0.04320.2474-0.01270.28-6.8467-13.2235-20.959
72.56560.6652-1.02221.7238-0.07013.1132-0.19840.48760.3711-0.33560.177-0.2031-0.06160.05550.03620.2428-0.0613-0.01130.29280.04480.26740.8975-8.9951-26.788
80.31670.1196-0.8740.3599-0.38262.5985-0.13691.0924-0.5436-0.3779-0.04090.09110.3541-0.20240.14120.4204-0.1266-0.01990.4387-0.1120.304-3.8466-19.1367-31.2012
94.27330.78650.06320.44060.17763.0557-0.38640.70370.539-0.81350.04960.0585-0.5336-0.71450.13120.5468-0.1132-0.12710.61880.06760.3708-2.5135-5.9201-36.1005
103.4551-0.2483-0.64614.430.7746.8617-0.38760.0646-0.0524-0.47450.5753-0.49520.32811.0461-0.16920.38210.0563-0.0130.3063-0.11640.4236-0.3257-38.0987-69.1534
110.59050.2739-0.71790.49120.1921.47540.40980.2528-0.546-0.1936-0.31711.03420.2997-0.61720.10740.2735-0.0261-0.07790.3417-0.05790.6301-28.2019-28.7999-62.2538
129.1661-1.2842-3.61320.30820.50561.5498-0.1369-0.5020.33340.1727-0.43551.3635-0.1202-0.72860.16150.2923-0.1103-0.06940.2775-0.47670.8689-24.9376-33.3292-63.2852
132.20980.3509-0.50662.03480.10633.0705-0.03170.1754-0.02480.0054-0.01540.1198-0.0942-0.24920.10680.23250.01850.00260.1847-0.04110.2463-16.1028-25.8314-66.2136
142.44820.4584-2.16461.18051.07075.4109-0.04960.0237-0.25540.7236-0.00590.14740.6004-0.19720.10550.5262-0.07420.07920.1917-0.03560.342-22.2129-37.1388-50.4871
150.68-0.8082-0.06491.1981-0.43991.09580.0258-0.12690.25110.0724-0.03880.2019-0.1908-0.1698-0.04390.46690.0093-0.0250.1721-0.0480.3769-17.731-13.8716-53.7549
161.4178-0.2909-0.081.29590.36192.2459-0.0396-0.2492-0.00380.1640.1336-0.06220.05440.14780.03240.2533-0.0072-0.02480.1884-0.01520.3055-10.3971-26.5699-55.2292
172.3344-1.18361.17762.5071-0.96842.8255-0.134-0.22570.10460.93950.04040.2798-0.0775-0.4156-0.04140.4363-0.00920.0320.196-0.02140.3218-19.3499-25.2551-48.9222
180.1268-0.15350.77070.7479-1.37494.8029-0.0019-0.62130.24670.65150.1953-0.50160.04670.37950.13180.45490.0094-0.09980.391-0.02450.3294-6.4354-24.9719-45.1193
191.72870.9848-0.65623.0747-0.1984.13460.056-0.26620.19960.6348-0.11740.2822-0.0837-0.367-0.09630.51090.00640.02570.2727-0.03450.2704-16.1619-21.2643-42.808
203.8939-0.7824-1.01784.4946-0.91539.27840.2433-0.92410.45060.3153-0.1783-0.4269-1.6044-0.19150.04010.33830.0412-0.03190.5707-0.10740.3254-4.0788-3.95760.2918
214.00853.00271.73327.97751.8391.90410.17860.0178-1.13430.58970.5339-0.1870.5454-0.0798-0.17070.34750.0083-0.03350.72020.28590.7172-19.2972-30.87358.2817
222.75220.8798-0.05871.90540.01271.7409-0.1089-0.5508-0.4048-0.10570.09250.00180.1568-0.0605-0.05170.22410.02080.01020.61260.08640.3308-18.7506-18.85274.1476
230.27360.4378-0.52621.1540.41944.32020.3138-1.21-0.79430.5963-0.0116-0.08720.5448-0.0233-0.3120.32110.0538-0.23221.68890.46960.3022-10.4296-25.32420.1825
240.2199-0.6017-0.03791.8546-0.16610.33390.1003-0.6855-0.14640.14720.02270.7741-0.0268-0.25170.0801-0.0615-0.01290.16041.61650.23670.4294-31.7738-16.489116.6351
250.5696-0.49070.41212.27170.17772.66020.2236-1.426-0.1290.5477-0.10230.3049-0.09850.0905-0.07650.369-0.02710.04211.14460.07880.2583-19.3019-14.734717.0219
260.4805-0.09470.56961.26070.21331.425-0.132-1.06170.32450.7330.0890.03840.08980.0831-0.08930.691-0.05670.06041.3666-0.03060.3052-22.5517-11.903825.999
273.6635-0.3668-0.44374.25060.17596.3623-0.3936-0.1463-0.1899-0.5217-0.2810.008-0.437-1.39910.08830.50490.1188-0.08530.4546-0.08870.3173-20.6946-22.6794-77.9011
283.83031.84380.02573.41910.1317-0.02480.2628-0.08110.0752-0.1482-0.1893-0.73780.05090.3090.00220.51310.01910.15290.4306-0.01570.53511.668-3.5192-85.0012
291.119-0.05130.1851.4072-0.03412.43760.1364-0.00220.1275-0.3749-0.0196-0.5143-0.08090.181-0.08710.49520.0710.12970.23170.00560.3708-9.6612-6.4364-80.9365
301.08140.1434-0.5941.2224-1.524.29450.18390.7355-0.0433-0.70330.1331-0.67320.56180.85960.00220.82560.15630.26340.620.00010.4771-1.3682-12.9917-96.7125
311.3641-0.4699-0.18851.7191.40511.1696-0.0050.31280.732-0.3951-0.17220.0197-0.4139-0.02530.11091.22380.15890.08640.37510.08980.564-14.63586.2274-93.1698
321.7227-0.3390.19250.19960.53932.3835-0.03960.54570.3363-1.0560.16560.11560.06-0.0771-0.13790.85270.09610.10020.3590.02350.2547-13.7431-6.6446-93.8413
330.0721-0.0542-0.16450.30371.00433.3449-0.1740.58550.3142-0.85240.40490.1106-0.5754-0.3773-0.09940.80350.11310.00310.71150.0320.3182-20.2513-8.6092-102.3247
342.7303-1.6233-0.72071.82441.64762.1080.40381.78511.1693-0.95310.0187-0.4258-0.56980.0879-0.23761.04060.14580.130.85050.21130.4237-12.8258-1.172-104.343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 42 )A30 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 55 )A43 - 55
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 66 )A56 - 66
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 95 )A67 - 95
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 110 )A96 - 110
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 142 )A111 - 142
7X-RAY DIFFRACTION7chain 'A' and (resid 143 through 172 )A143 - 172
8X-RAY DIFFRACTION8chain 'A' and (resid 173 through 194 )A173 - 194
9X-RAY DIFFRACTION9chain 'A' and (resid 195 through 217 )A195 - 217
10X-RAY DIFFRACTION10chain 'B' and (resid 30 through 42 )B30 - 42
11X-RAY DIFFRACTION11chain 'B' and (resid 43 through 55 )B43 - 55
12X-RAY DIFFRACTION12chain 'B' and (resid 56 through 66 )B56 - 66
13X-RAY DIFFRACTION13chain 'B' and (resid 67 through 95 )B67 - 95
14X-RAY DIFFRACTION14chain 'B' and (resid 96 through 110 )B96 - 110
15X-RAY DIFFRACTION15chain 'B' and (resid 111 through 125 )B111 - 125
16X-RAY DIFFRACTION16chain 'B' and (resid 126 through 156 )B126 - 156
17X-RAY DIFFRACTION17chain 'B' and (resid 157 through 172 )B157 - 172
18X-RAY DIFFRACTION18chain 'B' and (resid 173 through 186 )B173 - 186
19X-RAY DIFFRACTION19chain 'B' and (resid 187 through 217 )B187 - 217
20X-RAY DIFFRACTION20chain 'C' and (resid 28 through 42 )C28 - 42
21X-RAY DIFFRACTION21chain 'C' and (resid 43 through 59 )C43 - 59
22X-RAY DIFFRACTION22chain 'C' and (resid 60 through 95 )C60 - 95
23X-RAY DIFFRACTION23chain 'C' and (resid 96 through 110 )C96 - 110
24X-RAY DIFFRACTION24chain 'C' and (resid 111 through 125 )C111 - 125
25X-RAY DIFFRACTION25chain 'C' and (resid 126 through 172 )C126 - 172
26X-RAY DIFFRACTION26chain 'C' and (resid 173 through 217 )C173 - 217
27X-RAY DIFFRACTION27chain 'D' and (resid 30 through 42 )D30 - 42
28X-RAY DIFFRACTION28chain 'D' and (resid 43 through 59 )D43 - 59
29X-RAY DIFFRACTION29chain 'D' and (resid 60 through 95 )D60 - 95
30X-RAY DIFFRACTION30chain 'D' and (resid 96 through 110 )D96 - 110
31X-RAY DIFFRACTION31chain 'D' and (resid 111 through 125 )D111 - 125
32X-RAY DIFFRACTION32chain 'D' and (resid 126 through 172 )D126 - 172
33X-RAY DIFFRACTION33chain 'D' and (resid 173 through 186 )D173 - 186
34X-RAY DIFFRACTION34chain 'D' and (resid 187 through 217 )D187 - 217

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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