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- EMDB-18198: Helical reconstruction of the relaxed thick filament from FIB mil... -

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Entry
Database: EMDB / ID: EMD-18198
TitleHelical reconstruction of the relaxed thick filament from FIB milled left ventricular mouse myofibrils
Map dataHelical reconstruction of the relaxed thick filament from FIB-milled mouse left ventricular myofibrils
Sample
  • Cell: Relaxed thick filament; A-band region; C-type super-repeat
    • Protein or peptide: Myosin-7
    • Protein or peptide: Myosin light chain 3
    • Protein or peptide: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
    • Protein or peptide: Titin
    • Protein or peptide: Myosin binding protein C, cardiac
KeywordsMammalian / Muscle / Thick filament / Cardiac / MOTOR PROTEIN
Function / homology
Function and homology information


forward locomotion / heart growth / striated muscle cell development / regulation of relaxation of cardiac muscle / muscle cell fate specification / Striated Muscle Contraction / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / sarcomerogenesis / structural molecule activity conferring elasticity ...forward locomotion / heart growth / striated muscle cell development / regulation of relaxation of cardiac muscle / muscle cell fate specification / Striated Muscle Contraction / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / contractile muscle fiber / skeletal muscle myosin thick filament assembly / cardiac myofibril / muscle myosin complex / regulation of striated muscle contraction / cardiac myofibril assembly / muscle filament sliding / muscle alpha-actinin binding / detection of muscle stretch / ventricular system development / regulation of the force of heart contraction / transition between fast and slow fiber / muscle cell development / myosin filament / cardiac muscle tissue morphogenesis / myosin II complex / adult heart development / cardiac muscle tissue development / cardiac muscle hypertrophy in response to stress / cardiac muscle hypertrophy / M band / actinin binding / I band / cardiac muscle cell development / myosin complex / A band / sarcomere organization / structural constituent of muscle / microfilament motor activity / ankyrin binding / ventricular cardiac muscle tissue morphogenesis / myofibril / heart contraction / intracellular non-membrane-bounded organelle / positive regulation of the force of heart contraction / skeletal muscle thin filament assembly / cytoskeletal motor activity / striated muscle thin filament / skeletal muscle contraction / actin monomer binding / striated muscle contraction / somitogenesis / ATP metabolic process / stress fiber / heart morphogenesis / protein kinase A signaling / cardiac muscle contraction / regulation of heart rate / sarcomere / post-embryonic development / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / structural constituent of cytoskeleton / negative regulation of cell growth / Z disc / response to calcium ion / : / actin filament binding / actin cytoskeleton / heart development / protein tyrosine kinase activity / in utero embryonic development / protease binding / cytoskeleton / calmodulin binding / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / protein-containing complex binding / positive regulation of gene expression / protein kinase binding / enzyme binding / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain ...PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / EF hand / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / EF-hand, calcium binding motif / Immunoglobulin V-set domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Titin / Myosin light chain 3 / Myosin regulatory light chain 2, ventricular/cardiac muscle isoform / Myosin binding protein C, cardiac / Myosin-7
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 18.0 Å
AuthorsTamborrini D / Raunser S
Funding support Germany, European Union, United Kingdom, 5 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)856118European Union
Wellcome Trust201543/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R003106/1 United Kingdom
European Molecular Biology Organization (EMBO)European Union
CitationJournal: Nature / Year: 2023
Title: Structure of the native myosin filament in the relaxed cardiac sarcomere.
Authors: Davide Tamborrini / Zhexin Wang / Thorsten Wagner / Sebastian Tacke / Markus Stabrin / Michael Grange / Ay Lin Kho / Martin Rees / Pauline Bennett / Mathias Gautel / Stefan Raunser /
Abstract: The thick filament is a key component of sarcomeres, the basic units of striated muscle. Alterations in thick filament proteins are associated with familial hypertrophic cardiomyopathy and other ...The thick filament is a key component of sarcomeres, the basic units of striated muscle. Alterations in thick filament proteins are associated with familial hypertrophic cardiomyopathy and other heart and muscle diseases. Despite the central importance of the thick filament, its molecular organization remains unclear. Here we present the molecular architecture of native cardiac sarcomeres in the relaxed state, determined by cryo-electron tomography. Our reconstruction of the thick filament reveals the three-dimensional organization of myosin, titin and myosin-binding protein C (MyBP-C). The arrangement of myosin molecules is dependent on their position along the filament, suggesting specialized capacities in terms of strain susceptibility and force generation. Three pairs of titin-α and titin-β chains run axially along the filament, intertwining with myosin tails and probably orchestrating the length-dependent activation of the sarcomere. Notably, whereas the three titin-α chains run along the entire length of the thick filament, titin-β chains do not. The structure also demonstrates that MyBP-C bridges thin and thick filaments, with its carboxy-terminal region binding to the myosin tails and directly stabilizing the OFF state of the myosin heads in an unforeseen manner. These results provide a foundation for future research investigating muscle disorders involving sarcomeric components.
History
DepositionAug 14, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18198.png

Downloads & links

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Map

FileDownload / File: emd_18198.map.gz / Format: CCP4 / Size: 196.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical reconstruction of the relaxed thick filament from FIB-milled mouse left ventricular myofibrils
Voxel sizeX=Y=Z: 5.83 Å
Density
Contour LevelBy AUTHOR: 2.41
Minimum - Maximum0.0 - 13.521652
Average (Standard dev.)0.027506957 (±0.3870183)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions372372372
Spacing372372372
CellA=B=C: 2168.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Relaxed thick filament; A-band region; C-type super-repeat

EntireName: Relaxed thick filament; A-band region; C-type super-repeat
Components
  • Cell: Relaxed thick filament; A-band region; C-type super-repeat
    • Protein or peptide: Myosin-7
    • Protein or peptide: Myosin light chain 3
    • Protein or peptide: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
    • Protein or peptide: Titin
    • Protein or peptide: Myosin binding protein C, cardiac

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Supramolecule #1: Relaxed thick filament; A-band region; C-type super-repeat

SupramoleculeName: Relaxed thick filament; A-band region; C-type super-repeat
type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #5, #4
Details: Single asymmetrical unit from the relaxed thick filament obtained from FIB milled left ventricular mouse myofibrils
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Myosin-7

MacromoleculeName: Myosin-7 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 223.226531 KDa
SequenceString: MADAEMAAFG AAAPFLRKSE KERLEAQTRP FDLKKDVFVP DDKEEFVKAK IVSREGGKVT AETENGKTVT VKEDQVMQQN PPKFDKIED MAMLTFLHEP AVLYNLKERY ASWMIYTYSG LFCVTVNPYK WLPVYNAEVV AAYRGKKRSE APPHIFSISD N AYQYMLTD ...String:
MADAEMAAFG AAAPFLRKSE KERLEAQTRP FDLKKDVFVP DDKEEFVKAK IVSREGGKVT AETENGKTVT VKEDQVMQQN PPKFDKIED MAMLTFLHEP AVLYNLKERY ASWMIYTYSG LFCVTVNPYK WLPVYNAEVV AAYRGKKRSE APPHIFSISD N AYQYMLTD RENQSILITG ESGAGKTVNT KRVIQYFAVI AAIGDRSKKD QTPGKGTLED QIIQANPALE AFGNAKTVRN DN SSRFGKF IRIHFGATGK LASADIETYL LEKSRVIFQL KAERDYHIFY QILSNKKPEL LDMLLITNNP YDYAFISQGE TTV ASIDDS EELMATDSAF DVLGFTPEEK NSIYKLTGAI MHFGNMKFKQ KQREEQAEPD GTEEADKSAY LMGLNSADLL KGLC HPRVK VGNEYVTKGQ NVQQVSYAIG ALAKSVYEKM FNWMVTRINA TLETKQPRQY FIGVLDIAGF EIFDFNSFEQ LCINF TNEK LQQFFNHHMF VLEQEEYKKE GIEWTFIDFG MDLQACIDLI EKPMGIMSIL EEECMFPKAT DMTFKAKLYD NHLGKS NNF QKPRNVKGKQ EAHFSLVHYA GTVDYNILGW LQKNKDPLNE TVVGLYQKSS LKLLSNLFAN YAGADAPADK GKGKAKK GS SFQTVSALHR ENLNKLMTNL RSTHPHFVRC IIPNETKSPG VMDNPLVMHQ LRCNGVLEGI RICRKGFPNR ILYGDFRQ R YRILNPAAIP EGQFIDSRKG AEKLLGSLDI DHNQYKFGHT KVFFKAGLLG LLEEMRDERL SRIITRIQAQ SRGVLSRME FKKLLERRDS LLIIQWNIRA FMGVKNWPWM KLYFKIKPLL KSAETEKEMA TMKEEFGRVK DALEKSEARR KELEEKMVSL LQEKNDLQL QVQAEQDNLA DAEERCDQLI KNKIQLEAKV KEMTERLEDE EEMNAELTAK KRKLEDECSE LKRDIDDLEL T LAKVEKEK HATENKVKNL TEEMAGLDEI IVKLTKEKKA LQEAHQQALD DLQAEEDKVN TLTKAKVKLE QQVDDLEGSL EQ EKKVRMD LERAKRKLEG DLKLTQESIM DLENDKQQLD ERLKKKDFEL NALNARIEDE QALGSQLQKK LKELQARIEE LEE ELEAER TARAKVEKLR SDLSRELEEI SERLEEAGGA TSVQIEMNKK REAEFQKMRR DLEEATLQHE ATAAALRKKH ADSV AELGE QIDNLQRVKQ KLEKEKSEFK LELDDVTSNM EQIIKAKANL EKMCRTLEDQ MNEHRSKAEE TQRSVNDLTS QRAKL QTEN GELSRQLDEK EALISQLTRG KLTYTQQLED LKRQLEEEVK AKNALAHALQ SARHDCDLLR EQYEEETEAK AELQRV LSK ANSEVAQWRT KYETDAIQRT EELEEAKKKL AQRLQDAEEA VEAVNAKCSS LEKTKHRLQN EIEDLMVDVE RSNAAAA AL DKKQRNFDKI LAEWKQKYEE SQSELESSQK EARSLSTELF KLKNAYEESL EHLETFKREN KNLQEEISDL TEQLGSTG K SIHELEKIRK QLEAEKLELQ SALEEAEASL EHEEGKILRA QLEFNQIKAE IERKLAEKDE EMEQAKRNHL RMVDSLQTS LDAETRSRNE ALRVKKKMEG DLNEMEIQLS HANRMAAEAQ KQVKSLQSLL KDTQIQLDDA VRANDDLKEN IAIVERRNNL LQAELEELR AVVEQTERSR KLAEQELIET SERVQLLHSQ NTSLINQKKK MDADLSQLQT EVEEAVQECR NAEEKAKKAI T DAAMMAEE LKKEQDTSAH LERMKKNMEQ TIKDLQHRLD EAEQIALKGG KKQLQKLEAR VRELENELEA EQKRNAESVK GM RKSERRI KELTYQTEED RKNLLRLQDL VDKLQLKVKA YKRQAEEAEE QANTNLSKFR KVQHELDEAE ERADIAESQV NKL RAKSRD IGAKGLNEE

UniProtKB: Myosin-7

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Macromolecule #2: Myosin light chain 3

MacromoleculeName: Myosin light chain 3 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 17.243553 KDa
SequenceString:
IEFTPEQIEE FKEAFLLFDR TPKGEMKITY GQCGDVLRAL GQNPTQAEVL RVLGKPKQEE LNSKMMDFET FLPMLQHISK NKDTGTYED FVEGLRVFDK EGNGTVMGAE LRHVLATLGE RLTEDEVEKL MAGQEDSNGC INYEAFVKHI MAS

UniProtKB: Myosin light chain 3

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Macromolecule #3: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform

MacromoleculeName: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform
type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.259512 KDa
SequenceString:
KKRIEGGSSN VFSMFEQTQI QEFKEAFTIM DQNRDGFIDK NDLRDTFAAL GRVNVKNEEI DEMIKEAPGP INFTVFLTMF GEKLKGADP EETILNAFKV FDPEGKGSLK ADYVREMLTT QAERFSKEEI DQMFAAFPPD VTGNLDYKNL VHIITHGEEK D

UniProtKB: Myosin regulatory light chain 2, ventricular/cardiac muscle isoform

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Macromolecule #4: Myosin binding protein C, cardiac

MacromoleculeName: Myosin binding protein C, cardiac / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 44.777125 KDa
SequenceString: PIGPPGEPTH LAVEDVSDTT VSLKWRPPER VGAGGLDGYS VEYCQEGCSE WTPALQGLTE RTSMLVKDLP TGARLLFRVR AHNVAGPGG PIVTKEPVTV QEILQRPRLQ LPRHLRQTIQ KKVGEPVNLL IPFQGKPRPQ VTWTKEGQPL AGEEVSIRNS P TDTILFIR ...String:
PIGPPGEPTH LAVEDVSDTT VSLKWRPPER VGAGGLDGYS VEYCQEGCSE WTPALQGLTE RTSMLVKDLP TGARLLFRVR AHNVAGPGG PIVTKEPVTV QEILQRPRLQ LPRHLRQTIQ KKVGEPVNLL IPFQGKPRPQ VTWTKEGQPL AGEEVSIRNS P TDTILFIR AARRTHSGTY QVTVRIENME DKATLILQIV DKPSPPQDIR IVETWGFNVA LEWKPPQDDG NTEIWGYTVQ KA DKKTMEW FTVLEHYRRT HCVVSELIIG NGYYFRVFSH NMVGSSDKAA ATKEPVFIPR PGITYEPPKY KALDFSEAPS FTQ PLANRS IIAGYNAILC CAVRGSPKPK ISWFKNGLDL GEDARFRMFC KQGVLTLEIR KPCPYDGGVY VCRATNLQGE AQCE

UniProtKB: Myosin binding protein C, cardiac

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Macromolecule #5: Titin

MacromoleculeName: Titin / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 118.76632 KDa
SequenceString: DPCDPPGRPE AIVITRNSVT LKWKKPVYDG GSKITGYIVE KKDLPDGRWM KASFTNVVET EFTVTGLVED QRYEFRVIAR NAADNFSEP SESSGAITAR DEIDAPNASL DPKYRDVIIV HAGETFVLEA DIRGKPIPDI IWSKDGNELE ETAARMEIKS T LQKTTLIV ...String:
DPCDPPGRPE AIVITRNSVT LKWKKPVYDG GSKITGYIVE KKDLPDGRWM KASFTNVVET EFTVTGLVED QRYEFRVIAR NAADNFSEP SESSGAITAR DEIDAPNASL DPKYRDVIIV HAGETFVLEA DIRGKPIPDI IWSKDGNELE ETAARMEIKS T LQKTTLIV KDCIRTDGGQ YTLKLSNVGG TKTIPITVKV LDRPGPPEGP LKVTGVTAEK CYLAWNPPLQ DGGASISHYI IE KRETSRL SWTQVSNEVQ ALNYKVTKLL PGNEYIFRVM AVNKYGIGEA LESEPVIACN PYKRPGPPST PEASAITKDS MVL TWTRPV DDGGAEIEGY ILEKRDKEGI RWTKCNKKTL TDLRFRVTGL TEGHSYEFRV AAENAAGVGE PSEPSVFYRA CDAL YPPGP PSNPKVTDTS RSSVSLAWNK PIYDGGAPVR GYVIELKKAA ADEWTTCTPP SGLQGKQFTV TKLKENTEYN FRICA FNTE GVGEPATIPG SVVAQERMEA PEIELDADLR KVVTLRASAT LRLFVTIKGR PEPEVKWEKA EGILTERAQI EVTSSY TML VIDNVTRFDS GRYNLTLENN SGSKTAFVNV RVLDSPSAPV NLTIREVKKD SVTLSWEPPL IDGGAKITNY IVEKRET TR KAYATITNNC TKNTFKIENL QEGCSYYFRV LASNEYGIGL PAETAEPVKV SEPPLPPGRV TLVDVTRNTA TIKWEKPE S DGGSKITGYV VEMQTKGSEK WSACTQVKTL ETTISGLTAG EEYVFRVAAV NEKGRSDPRQ LGVPVIAKDI EIKPSVELP FNTFNVKAND QLKIDIPFKG RPQATVAWKK DGQVLRETTR VNVASSKTVT TLSIKEASRE DVGTYELCVS NTAGSITVPI TVIVLDRPG PPGPIRIDEV SCDNVSISWN PPEYDGGCQI SNYIVEKRET TSTTWQVVSQ AVARTSIKIV RLTTGSEYQF R VCAENRYG KSSYSESSAV VAEYPFSPPG PPGTPKVVHA TKSTMVVSWQ VPVNDGGSQV IGYHLEYKER SSILWSKANK VL IADTQMK VSGLDEGLMY EYRVYAENIA GIGKCSKACE PV

UniProtKB: Titin

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.1
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 89 / Number images used: 67492
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Helical parameters - Δz: 430.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 0 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION
Details: Helical reconstruction containing 4.5x repeats extrapolated from a 3x repeat reconstruction (EMD-18146)
Number subtomograms used: 1589

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Atomic model buiding 1

Initial model(Chain: AlphaFold, SwissModel)
Output model

PDB-8q6t:
Helical reconstruction of the relaxed thick filament from FIB milled left ventricular mouse myofibrils

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