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- PDB-8v57: Complex of murine cathepsin K with bound cystatin C inhibitor -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8v57
TitleComplex of murine cathepsin K with bound cystatin C inhibitor
Components
  • Cathepsin K
  • Cystatin-C
KeywordsHYDROLASE / complex / inhibitor / protease / collagenase
Function / homology
Function and homology information


RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Activation of Matrix Metalloproteinases / Collagen degradation / Trafficking and processing of endosomal TLR / contractile muscle fiber / cathepsin K / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Degradation of the extracellular matrix / negative regulation of cartilage development ...RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Activation of Matrix Metalloproteinases / Collagen degradation / Trafficking and processing of endosomal TLR / contractile muscle fiber / cathepsin K / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Degradation of the extracellular matrix / negative regulation of cartilage development / peptidase inhibitor activity / MHC class II antigen presentation / thyroid hormone generation / proteoglycan binding / collagen catabolic process / fibronectin binding / basement membrane / cysteine-type endopeptidase inhibitor activity / bone resorption / collagen binding / multivesicular body / Neutrophil degranulation / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / positive regulation of DNA replication / cell projection / : / cellular response to oxidative stress / protease binding / vesicle / nuclear membrane / lysosome / apical plasma membrane / axon / external side of plasma membrane / cysteine-type endopeptidase activity / neuronal cell body / positive regulation of cell population proliferation / perinuclear region of cytoplasm / extracellular space / nucleoplasm / cytoplasm
Similarity search - Function
Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase ...Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Cystatin-C / Cathepsin K
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPedersen, L.C. / Xu, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIC-ES102645 United States
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R01DE031273 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01AR070179 United States
CitationJournal: Matrix Biol. / Year: 2024
Title: Heparan sulfate selectively inhibits the collagenase activity of cathepsin K.
Authors: Zhang, X. / Luo, Y. / Hao, H. / Krahn, J.M. / Su, G. / Dutcher, R. / Xu, Y. / Liu, J. / Pedersen, L.C. / Xu, D.
History
DepositionNov 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin K
B: Cathepsin K
C: Cystatin-C
D: Cystatin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,14518
Polymers74,1784
Non-polymers1,96814
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.930, 179.610, 73.352
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Cathepsin K


Mass: 23662.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctsk / Plasmid: pUNO1 / Cell line (production host): HEK293 freestyle / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: P55097
#2: Protein Cystatin-C


Mass: 13426.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cst3 / Plasmid: pET21b / Details (production host): coexpressed with pGro7 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami-B / References: UniProt: P21460

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Sugars , 1 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 25 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 5mg/ml CtsK+Cystatin C co-purified with 12mer GlcNS6S-GlcA-GlcNS3S6S-Ido2S-GlcNS6S-Ido2S-GlcNS6S-Ido2S-GlcNS6S-Ido2S-GlcNS6S-GlcA-pNP, sodium citrate, barium chloride, ammonium sulfate, PEG-4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 30916 / % possible obs: 92.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 72.6 Å2 / CC1/2: 1 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Rsym value: 0.059 / Net I/σ(I): 7.3
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.67 / Num. unique obs: 1413 / CC1/2: 0.85 / Rpim(I) all: 0.305 / Rrim(I) all: 0.83 / Rsym value: 0.77 / % possible all: 86.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→38.35 Å / SU ML: 0.4494 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.0333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2579 1502 4.99 %
Rwork0.2286 28617 -
obs0.23 30119 92.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.4 Å2
Refinement stepCycle: LAST / Resolution: 2.75→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4904 0 115 13 5032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675111
X-RAY DIFFRACTIONf_angle_d0.72276936
X-RAY DIFFRACTIONf_chiral_restr0.0452747
X-RAY DIFFRACTIONf_plane_restr0.006902
X-RAY DIFFRACTIONf_dihedral_angle_d12.95671786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.840.50851100.45182207X-RAY DIFFRACTION79.76
2.84-2.940.3991230.34512313X-RAY DIFFRACTION82.41
2.94-3.060.37451360.30672631X-RAY DIFFRACTION95.18
3.06-3.20.35591440.27242677X-RAY DIFFRACTION95.37
3.2-3.370.30991400.26892671X-RAY DIFFRACTION96.83
3.37-3.580.30461420.29392695X-RAY DIFFRACTION95.81
3.58-3.850.25421420.21932679X-RAY DIFFRACTION95.4
3.85-4.240.24791420.19942687X-RAY DIFFRACTION95.06
4.24-4.850.1971370.17472618X-RAY DIFFRACTION92.29
4.85-6.110.21631290.20622458X-RAY DIFFRACTION85.49
6.11-38.350.22421570.20862981X-RAY DIFFRACTION98.46
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)
11.33549861752-0.9141149974260.627984989920.558284180379-0.4399279070120.0870359600757-0.19400738593-1.18343821957-1.664155269160.0186690403263-1.23685302713-1.992280877311.049042586971.15567499574-0.001064777747260.9511033405080.07829540512440.0833412764280.6870765136840.1638532271940.983044298058-10.3520746315-90.8565417567-4.52831890032
22.16148807332-1.05889915312-1.485883234451.90976370626-0.4074189098521.490195999510.112498637096-0.2943982755260.2769352837390.869978775792-0.4873475999760.32712756909-0.494731751424-0.105239131589-9.88110780672E-71.33361856265-0.144649048936-0.006053025464670.8359574942610.05489263278680.794629698082-38.8952737741-6.5868736497411.5970090199
31.85643656638-0.620186261583-0.2688184737630.936613635122-0.7842975208210.8600384505870.097724218695-0.1267381747960.6187676469020.547960564032-0.20635671241-0.812050782323-0.811252836033-0.03576895936-1.89584543822E-61.24790574189-0.0127668806988-0.05511698803010.7929383815950.03942533765120.787034274831-37.6480017664-4.550677009058.59295967007
40.0628035212815-0.0748664748429-0.07555617993750.03446389324240.05353081332060.03106954632330.6794803097580.934120675743-0.170298976543-0.700379324638-0.2754139559730.664486680469-0.614827430731-1.369842281912.24647431365E-52.72844122598-0.0857119672550.07809082538841.342371543730.03547734264461.25562061731-38.94816605436.0059491253427.8510880742
50.4967238751210.238753324167-1.253331111910.181463896898-0.1555123583160.4096441023370.3058937585050.2282627948460.4274911065150.811022116439-0.193584667921-0.588466462568-0.979812176383-0.05358517039681.05127920533E-71.7192208925-0.171394199464-0.2486301634150.912560916280.1239386828540.919315105407-34.6243672758-2.1615526623614.6394891651
61.12610111189-0.902393776533-1.14152813111.19950917618-0.0003975537964412.81364375586-0.249473386429-0.223034021394-1.079677304270.113072269782-0.371650959319-0.2676057944270.827635123526-0.2263646545962.17752159399E-60.902706571769-0.01151512096360.1016997143320.7618474289580.08361966760290.803738859423-41.2696699458-39.19642076133.1703577949
70.495818483037-0.332963941793-0.5535494780690.325041260829-0.09637163038810.467632099422-0.3209800059450.26061544866-0.553136373864-0.24647151708-0.148426853081-0.7037668249710.884420702607-0.03613658377751.67480969023E-60.7502582977650.08077638951360.08935906082450.6802576248150.1152318646570.846860616554-34.6866122415-38.5204209983-3.65071687387
80.229924888033-0.301169042430.00519080544590.4519442737030.1744479159120.480994480912-0.0196270223192-0.191519382514-0.433760725304-1.01199321389-0.904821162216-2.059867099460.110834631991.33621360526-0.07037380661760.4881113542780.2258687094530.1278016911560.7392151459650.2645091834881.03360005436-27.4296036405-35.0745895947-1.35037272919
90.1365574348680.2861943862-0.1057072690720.374116726597-0.1642284201690.07095009974320.09150593245060.735432649038-0.0100115080839-0.447751921443-0.198625569919-0.675773635374-0.5929484387620.853852626488-8.72370500335E-61.043445558240.06617058472560.1345071569420.8254552193910.2426081650271.04354376728-31.2421740123-21.7471270979-7.46185021237
101.3713584536-0.511595404732-1.141719134591.36263967816-0.1551952879090.933658512816-0.01654228103050.05008525871750.201358961471-0.431342389781-0.429444927911-1.1460531364-0.1713475612960.7921019426052.0848709423E-60.7298598777580.03710798620350.0982273190050.9098017613920.2023226476330.997309654352-24.9188388392-31.4540372982-4.75192370161
110.5759313842990.702911265478-0.8281553756820.692365956791-0.7216218720171.51077425317-0.302680082780.823047295675-0.516808451901-0.611792376685-0.09747443805590.08518319716980.465654287855-0.3262020585492.20715718005E-70.9108877268770.04064819120210.1539418446870.834932383848-0.0338568383810.8505204096-42.8826014298-38.0521299287-11.3184725481
123.11018495276-0.95792441479-0.5155364334684.319537060140.9806525842544.46543160959-0.05810863595440.120574040217-0.1482608720980.693439720876-0.3424216968380.25720490836-0.0942747693716-0.6262031541-3.99657651054E-80.6709789811180.0335174182110.09366692626520.753500879101-0.02729715254150.618795160085-49.0101990922-30.97191195411.99384722273
133.29425114511-1.89037599836-0.554736873912.728162280271.519105301541.728943779720.3323770888050.04194157252980.222090663994-0.0999726956136-0.1252141909310.151810442636-0.3781510522-0.237660647817.48558296487E-80.651327275030.05207362843520.06763352536420.6882536056810.05028899944650.767696453551-21.3887100119-60.9569364674-12.4394822249
143.62408540541-0.650274602441-0.4422871236414.458628505690.6581246517811.840183873310.2351711419010.06081498372350.2282576908850.266780367172-0.2176536001370.65668176432-0.460236872536-0.57882270619-6.31427303182E-80.5431141847180.09899489129040.03000547544560.6916633083910.03310958571620.848865667182-28.0316293131-61.7746439252-11.7701940907
153.00836612133-1.39982589964-0.9180900456944.271573975780.155839423554.122202327350.5236659059820.6622032503160.151750701169-0.937651231808-0.27420615512-0.108891169294-0.273981568033-0.181909235851.15789732446E-80.6663353876680.1608411804960.07105479380520.7247167377890.08359048557380.700505689739-14.6801720072-65.1348433981-24.9604603728
160.145819867377-0.138227210854-0.2388537680140.0895475940620.196397433490.3639666468831.0062963841.8689342619-0.183604824105-1.35719331078-0.7710594599530.7236410780660.450381811846-1.814206035390.009234711613970.671723663133-0.0377646947481-0.1937981928871.09328992084-0.02222196595271.01612883005-24.2395862413-80.0215003179-19.0938647128
170.535054298106-0.477121724772-0.3834629862370.629239603840.2435695133660.1690966061880.187990264566-0.02122718703660.0871741381333-0.545046335286-0.317579358672-0.3858422595140.7147937092660.06249599533734.29327214898E-60.8477193029960.160538390681-0.05098583054050.8474841519590.05638736877790.813565846458-5.594617097-91.4109495124-13.4980281681
180.00381584208915-0.0773615076388-0.02348077719690.20914926136-0.1954681352570.145834364893-0.759426544624-1.21818672119-0.268662172325-0.1538888046450.316560496102-0.2690137700231.085799777-0.2710397336697.05230925724E-61.189473355150.335458050007-0.162060257170.970164667559-0.00328216268471.12918541255-4.40020377251-101.812560574-7.83131574468
190.9855597176191.220894945020.9461753489761.586779287810.9328998449062.441745714590.2214007972790.177335234256-0.343535710260.09217361001990.1528959275580.06987349614911.010272435680.4219408469884.0670576834E-70.9068359104660.0919752423494-0.1449443636210.7413768502610.01381819123980.785891177825-10.5523995805-92.0787651267-11.882558774
200.190518290218-0.14619529701-0.1305678824250.124940363504-0.03575010594280.204960661563-0.3557306023310.0835206023998-0.5909148884970.304538026895-0.297121769168-0.3778292589940.366398817324-1.10491142004-4.45443521883E-61.533364228880.124195385213-0.1006405302221.16109828309-0.02163334111421.453272606181.07939537424-108.136414205-9.96954010376
210.526256144881-0.702354404528-0.6274442907430.5743781263510.4086719027771.96612601817-0.07591710894130.197799676362-0.509784307029-0.280679147214-0.0509467967937-0.4706973801541.548226633420.530886890323-0.03116851314180.7326274925630.0197418816576-0.087227445840.6769120751570.08216900445250.70220273524-8.82328961603-85.3229175836-10.0082379155
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 109 through 120 )CH109 - 120104 - 115
22chain 'D' and (resid 7 through 43 )DI7 - 431 - 37
33chain 'D' and (resid 44 through 70 )DI44 - 7038 - 64
44chain 'D' and (resid 71 through 80 )DI71 - 8065 - 74
55chain 'D' and (resid 81 through 120 )DI81 - 12075 - 114
66chain 'A' and (resid 0 through 24 )AA0 - 241 - 25
77chain 'A' and (resid 25 through 42 )AA25 - 4226 - 43
88chain 'A' and (resid 43 through 56 )AA43 - 5644 - 57
99chain 'A' and (resid 57 through 67 )AA57 - 6758 - 68
1010chain 'A' and (resid 68 through 102 )AA68 - 10269 - 103
1111chain 'A' and (resid 103 through 127 )AA103 - 127104 - 128
1212chain 'A' and (resid 128 through 215 )AA128 - 215129 - 216
1313chain 'B' and (resid 1 through 67 )BE1 - 671 - 67
1414chain 'B' and (resid 68 through 127 )BE68 - 12768 - 127
1515chain 'B' and (resid 128 through 215 )BE128 - 215128 - 215
1616chain 'C' and (resid 6 through 15 )CH6 - 151 - 10
1717chain 'C' and (resid 16 through 37 )CH16 - 3711 - 32
1818chain 'C' and (resid 38 through 50 )CH38 - 5033 - 45
1919chain 'C' and (resid 51 through 75 )CH51 - 7546 - 70
2020chain 'C' and (resid 76 through 93 )CH76 - 9371 - 88
2121chain 'C' and (resid 94 through 108 )CH94 - 10889 - 103

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • 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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