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- EMDB-28580: Structure of human ADAM10-Tspan15 complex bound to 11G2 vFab -

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Entry
Database: EMDB / ID: EMD-28580
TitleStructure of human ADAM10-Tspan15 complex bound to 11G2 vFab
Map dataMap post-processed with DeepEMhancer using the high resolution model
Sample
  • Complex: ADAM10-Tspan15-11G2 Fab complex
    • Complex: Disintegrin and metalloproteinase domain-containing protein 10 (E.C.3.4.24.81), Tetraspanin-15
      • Protein or peptide: Disintegrin and metalloproteinase domain-containing protein 10
      • Protein or peptide: Tetraspanin-15
    • Complex: 11G2 Fab Heavy Chain, 11G2 Fab Light Chain
      • Protein or peptide: 11G2 Fab Heavy Chain
      • Protein or peptide: 11G2 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
  • Ligand: ZINC ION
  • Ligand: 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsProtease / Metalloprotease / Tetraspanin / Sheddase / Adhesion / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of membrane protein ectodomain proteolysis / ADAM10 endopeptidase / constitutive protein ectodomain proteolysis / regulation of vasculature development / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / protein catabolic process at postsynapse / postsynapse organization / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant ...regulation of membrane protein ectodomain proteolysis / ADAM10 endopeptidase / constitutive protein ectodomain proteolysis / regulation of vasculature development / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / protein catabolic process at postsynapse / postsynapse organization / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / : / regulation of Notch signaling pathway / perinuclear endoplasmic reticulum / positive regulation of T cell chemotaxis / pore complex assembly / NOTCH4 Activation and Transmission of Signal to the Nucleus / tetraspanin-enriched microdomain / metallodipeptidase activity / negative regulation of cell adhesion / adherens junction organization / regulation of postsynapse organization / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / clathrin-coated vesicle / Golgi-associated vesicle / Signaling by EGFR / cochlea development / negative regulation of Notch signaling pathway / pore complex / amyloid precursor protein catabolic process / tertiary granule membrane / membrane protein ectodomain proteolysis / protein maturation / Collagen degradation / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / response to tumor necrosis factor / specific granule membrane / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Degradation of the extracellular matrix / Activated NOTCH1 Transmits Signal to the Nucleus / synaptic membrane / NOTCH3 Activation and Transmission of Signal to the Nucleus / integrin-mediated signaling pathway / protein localization to plasma membrane / Post-translational protein phosphorylation / adherens junction / protein processing / metalloendopeptidase activity / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SH3 domain binding / metallopeptidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / integrin binding / cell-cell signaling / cell junction / late endosome membrane / positive regulation of cell growth / endopeptidase activity / in utero embryonic development / postsynaptic density / molecular adaptor activity / nuclear body / positive regulation of cell migration / Amyloid fiber formation / axon / endoplasmic reticulum lumen / Golgi membrane / protein phosphorylation / negative regulation of gene expression / signaling receptor binding / focal adhesion / intracellular membrane-bounded organelle / dendrite / glutamatergic synapse / positive regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / Golgi apparatus / enzyme binding / cell surface / protein homodimerization activity / extracellular exosome / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / ADAM10, cysteine-rich domain / ADAM10/ADAM17 catalytic domain / Metallo-peptidase family M12B Reprolysin-like / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Disintegrin / Disintegrin domain profile. ...: / ADAM10, cysteine-rich domain / ADAM10/ADAM17 catalytic domain / Metallo-peptidase family M12B Reprolysin-like / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Disintegrin and metalloproteinase domain-containing protein 10 / Tetraspanin-15
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLipper CH / Blacklow SC
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 CA220340 United States
Other privateGift from Edward B. Goodnow
CitationJournal: Cell / Year: 2023
Title: Structural basis for membrane-proximal proteolysis of substrates by ADAM10.
Authors: Colin H Lipper / Emily D Egan / Khal-Hentz Gabriel / Stephen C Blacklow /
Abstract: The endopeptidase ADAM10 is a critical catalyst for the regulated proteolysis of key drivers of mammalian development, physiology, and non-amyloidogenic cleavage of APP as the primary α-secretase. ...The endopeptidase ADAM10 is a critical catalyst for the regulated proteolysis of key drivers of mammalian development, physiology, and non-amyloidogenic cleavage of APP as the primary α-secretase. ADAM10 function requires the formation of a complex with a C8-tetraspanin protein, but how tetraspanin binding enables positioning of the enzyme active site for membrane-proximal cleavage remains unknown. We present here a cryo-EM structure of a vFab-ADAM10-Tspan15 complex, which shows that Tspan15 binding relieves ADAM10 autoinhibition and acts as a molecular measuring stick to position the enzyme active site about 20 Å from the plasma membrane for membrane-proximal substrate cleavage. Cell-based assays of N-cadherin shedding establish that the positioning of the active site by the interface between the ADAM10 catalytic domain and the bound tetraspanin influences selection of the preferred cleavage site. Together, these studies reveal the molecular mechanism underlying ADAM10 proteolysis at membrane-proximal sites and offer a roadmap for its modulation in disease.
History
DepositionOct 14, 2022-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28580.png

Downloads & links

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Map

FileDownload / File: emd_28580.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap post-processed with DeepEMhancer using the high resolution model
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.108
Minimum - Maximum-0.019989852 - 1.7453501
Average (Standard dev.)0.00033253848 (±0.010510009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 396.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28580_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_28580_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : ADAM10-Tspan15-11G2 Fab complex

EntireName: ADAM10-Tspan15-11G2 Fab complex
Components
  • Complex: ADAM10-Tspan15-11G2 Fab complex
    • Complex: Disintegrin and metalloproteinase domain-containing protein 10 (E.C.3.4.24.81), Tetraspanin-15
      • Protein or peptide: Disintegrin and metalloproteinase domain-containing protein 10
      • Protein or peptide: Tetraspanin-15
    • Complex: 11G2 Fab Heavy Chain, 11G2 Fab Light Chain
      • Protein or peptide: 11G2 Fab Heavy Chain
      • Protein or peptide: 11G2 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM IONCalcium
  • Ligand: ZINC ION
  • Ligand: 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: ADAM10-Tspan15-11G2 Fab complex

SupramoleculeName: ADAM10-Tspan15-11G2 Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Disintegrin and metalloproteinase domain-containing protein 10 (E...

SupramoleculeName: Disintegrin and metalloproteinase domain-containing protein 10 (E.C.3.4.24.81), Tetraspanin-15
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: 11G2 Fab Heavy Chain, 11G2 Fab Light Chain

SupramoleculeName: 11G2 Fab Heavy Chain, 11G2 Fab Light Chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Disintegrin and metalloproteinase domain-containing protein 10

MacromoleculeName: Disintegrin and metalloproteinase domain-containing protein 10
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ADAM10 endopeptidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.47734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKTT SAEKNTCQLY IQTDHLFFKY YGTREAVIAQ ISSHVKAIDT IYQTTDFSGI RNISFMVKRI RINTTADEKD PTNPFRFPN IGVEKFLELN SEQNHDDYCL AYVFTDRDFD DGVLGLAWVG APSGSSGGIC EKSKLYSDGK KKSLNTGIIT V QNYGSHVP ...String:
DYKDDDDKTT SAEKNTCQLY IQTDHLFFKY YGTREAVIAQ ISSHVKAIDT IYQTTDFSGI RNISFMVKRI RINTTADEKD PTNPFRFPN IGVEKFLELN SEQNHDDYCL AYVFTDRDFD DGVLGLAWVG APSGSSGGIC EKSKLYSDGK KKSLNTGIIT V QNYGSHVP PKVSHITFAH EVGHNFGSPH DSGTECTPGE SKNLGQKENG NYIMYARATS GDKLNNNKFS LCSIRNISQV LE KKRNNCF VESGQPICGN GMVEQGEECD CGYSDQCKDE CCFDANQPEG RKCKLKPGKQ CSPSQGPCCT AQCAFKSKSE KCR DDSDCA REGICNGFTA LCPASDPKPN FTDCNRHTQV CINGQCAGSI CEKYGLEECT CASSDGKDDK ELCHVCCMKK MDPS TCAST GSVQWSRHFS GRTITLQPGS PCNDFRGYCD VFMRCRLVDA DGPLARLKKA IFSPELYENI AEWIVAHWWA VLLMG IALI MLMAGFIKIC SVHTPSSNPK LPPPKPLPGT LKRRRPPQPI QQPQRQRPRE SYQMGHMRR

UniProtKB: Disintegrin and metalloproteinase domain-containing protein 10

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Macromolecule #2: Tetraspanin-15

MacromoleculeName: Tetraspanin-15 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.740469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHDDD DKMPRGDSEQ VRYCARFSYL WLKFSLIIYS TVFWLIGALV LSVGIYAEVE RQKYKTLESA FLAPAIILIL LGVVMFMVS FIGVLASLRD NLYLLQAFMY ILGICLIMEL IGGVVALTFR NQTIDFLNDN IRRGIENYYD DLDFKNIMDF V QKKFKCCG ...String:
MHHHHHHDDD DKMPRGDSEQ VRYCARFSYL WLKFSLIIYS TVFWLIGALV LSVGIYAEVE RQKYKTLESA FLAPAIILIL LGVVMFMVS FIGVLASLRD NLYLLQAFMY ILGICLIMEL IGGVVALTFR NQTIDFLNDN IRRGIENYYD DLDFKNIMDF V QKKFKCCG GEDYRDWSKN QYHDCSAPGP LACGVPYTCC IRNTTEVVNT MCGYKTIDKE RFSVQDVIYV RGCTNAVIIW FM DNYTIMA GILLGILLPQ FLGVLLTLLY ITRVEDIIME HSVTDGLLGP GAKPSVEAAG TGCCLCYPN

UniProtKB: Tetraspanin-15

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Macromolecule #3: 11G2 Fab Heavy Chain

MacromoleculeName: 11G2 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.135105 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLKESGPG LVAPSQSLSI TCTVSGFSLT GYGVNWVRQP PGKGLEWLGV IWGDGTTDYQ STLKSRLSIS KDNSKSQVFL KMNSLQTVD TARYYCARDG DYGRLDYWGQ GTTLTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN S GSLSSGVH ...String:
QVQLKESGPG LVAPSQSLSI TCTVSGFSLT GYGVNWVRQP PGKGLEWLGV IWGDGTTDYQ STLKSRLSIS KDNSKSQVFL KMNSLQTVD TARYYCARDG DYGRLDYWGQ GTTLTVSSAK TTPPSVYPLA PGSAAQTNSM VTLGCLVKGY FPEPVTVTWN S GSLSSGVH TFPAVLQSDL YTLSSSVTVP SSTWPSETVT CNVAHPASST KVDKKIVPRD CLEVLFQ

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Macromolecule #4: 11G2 Fab Light Chain

MacromoleculeName: 11G2 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.185803 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIVLTQSPAI MSASLGERVT MTCTVSSSVS SGYLHWYQQK SGSSPKLWIY STSNLASGVP ARFSGSGSGT SYSLTISSMG AEDAATYYC HQYRRSPLTF GAGTKLEIKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD ...String:
QIVLTQSPAI MSASLGERVT MTCTVSSSVS SGYLHWYQQK SGSSPKLWIY STSNLASGVP ARFSGSGSGT SYSLTISSMG AEDAATYYC HQYRRSPLTF GAGTKLEIKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD SKDSTYSMSS TLTLTKDEYE RHNSYTCEAT HKTSTSPIVK SFNRNECLEV LFQ

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #10: 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L...

MacromoleculeName: 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE
type: ligand / ID: 10 / Number of copies: 1 / Formula: BAT
Molecular weightTheoretical: 477.64 Da
Chemical component information

ChemComp-BAT:
4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE / inhibitor*YM / Batimastat

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Macromolecule #11: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 11 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMsodium chlorideNaClSodium chloride
0.03 %glyco-diosgenin (GDN)
0.003 %cholesteryl hemisuccinate
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 7 seconds with a blot force of 15.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 10037 / Average exposure time: 1.3 sec. / Average electron dose: 51.99 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6be6


Details: PDB 6BE6 was used for the initial model of ADAM10, 6BDZ was used for 11G2 vFab
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 178031

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-8esv:
Structure of human ADAM10-Tspan15 complex bound to 11G2 vFab

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