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- EMDB-29305: Cryo-EM structure of RNase-treated RESC-A in trypanosomal RNA editing -

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Basic information

Entry
Database: EMDB / ID: EMD-29305
TitleCryo-EM structure of RNase-treated RESC-A in trypanosomal RNA editing
Map data
Sample
  • Complex: RESC5-tagged isolate with RNase treatment
    • Protein or peptide: RNA-editing substrate-binding complex protein 1 (RESC1)
    • Protein or peptide: RNA-editing substrate-binding complex protein 2 (RESC2)
    • Protein or peptide: RNA-editing substrate-binding complex protein 3 (RESC3)
    • Protein or peptide: RNA-editing substrate-binding complex protein 4 (RESC4)
    • Protein or peptide: RNA-editing substrate-binding complex protein 5 (RESC5)
    • Protein or peptide: RNA-editing substrate-binding complex protein 6 (RESC6)
KeywordsHEAT repeat / trypanosoma / RNA editing substrate binding complex / gRNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


regulation of mitochondrial mRNA stability / mitochondrial RNA modification / mitochondrial mRNA processing / RNA modification / RNA stabilization / mitochondrial mRNA editing complex / ribonucleoprotein granule / mitochondrial RNA processing / RNA metabolic process / kinetoplast ...regulation of mitochondrial mRNA stability / mitochondrial RNA modification / mitochondrial mRNA processing / RNA modification / RNA stabilization / mitochondrial mRNA editing complex / ribonucleoprotein granule / mitochondrial RNA processing / RNA metabolic process / kinetoplast / RNA processing / mitochondrial matrix / mRNA binding / mitochondrion / RNA binding / cytoplasm
Similarity search - Function
Mitochondrial guide RNA binding complex subunit 2 / Mitochondrial RNA binding protein / Mitochondrial RNA binding complex 1 subunit / Mitochondrial RNA binding protein / Guide RNA associated protein, GAP2 / Guide RNA binding protein
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLiu S / Wang H / Li X / Zhang F / Lee JKJ / Li Z / Yu C / Zhao X / Hu JJ / Suematsu T ...Liu S / Wang H / Li X / Zhang F / Lee JKJ / Li Z / Yu C / Zhao X / Hu JJ / Suematsu T / Alvarez-Cabrera AL / Liu Q / Zhang L / Huang L / Aphasizheva I / Aphasizhev R / Zhou ZH
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1AI101057 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI152408 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
CitationJournal: Science / Year: 2023
Title: Structural basis of gRNA stabilization and mRNA recognition in trypanosomal RNA editing.
Authors: Shiheng Liu / Hong Wang / Xiaorun Li / Fan Zhang / Jane K J Lee / Zihang Li / Clinton Yu / Jason J Hu / Xiaojing Zhao / Takuma Suematsu / Ana L Alvarez-Cabrera / Qiushi Liu / Liye Zhang / ...Authors: Shiheng Liu / Hong Wang / Xiaorun Li / Fan Zhang / Jane K J Lee / Zihang Li / Clinton Yu / Jason J Hu / Xiaojing Zhao / Takuma Suematsu / Ana L Alvarez-Cabrera / Qiushi Liu / Liye Zhang / Lan Huang / Inna Aphasizheva / Ruslan Aphasizhev / Z Hong Zhou /
Abstract: In , the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)-programmed editing to recode cryptic mitochondrial ...In , the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)-programmed editing to recode cryptic mitochondrial transcripts into messenger RNAs (mRNAs). The mechanism of information transfer from gRNA to mRNA is unclear owing to a lack of high-resolution structures for these complexes. With cryo-electron microscopy and functional studies, we have captured gRNA-stabilizing RESC-A and gRNA-mRNA-binding RESC-B and RESC-C particles. RESC-A sequesters gRNA termini, thus promoting hairpin formation and blocking mRNA access. The conversion of RESC-A into RESC-B or -C unfolds gRNA and allows mRNA selection. The ensuing gRNA-mRNA duplex protrudes from RESC-B, likely exposing editing sites to RECC-catalyzed cleavage, uridine insertion or deletion, and ligation. Our work reveals a remodeling event facilitating gRNA-mRNA hybridization and assembly of a macromolecular substrate for the editosome's catalytic modality.
History
DepositionDec 26, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29305.png

Downloads & links

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Map

FileDownload / File: emd_29305.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.872 Å		1.06 Å/pix.
x 256 pix.
= 271.872 Å		1.06 Å/pix.
x 256 pix.
= 271.872 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.062 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.06874664 - 0.118634805
Average (Standard dev.)0.0003826357 (±0.0038373498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.872 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29305_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29305_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : RESC5-tagged isolate with RNase treatment

EntireName: RESC5-tagged isolate with RNase treatment
Components
  • Complex: RESC5-tagged isolate with RNase treatment
    • Protein or peptide: RNA-editing substrate-binding complex protein 1 (RESC1)
    • Protein or peptide: RNA-editing substrate-binding complex protein 2 (RESC2)
    • Protein or peptide: RNA-editing substrate-binding complex protein 3 (RESC3)
    • Protein or peptide: RNA-editing substrate-binding complex protein 4 (RESC4)
    • Protein or peptide: RNA-editing substrate-binding complex protein 5 (RESC5)
    • Protein or peptide: RNA-editing substrate-binding complex protein 6 (RESC6)

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Supramolecule #1: RESC5-tagged isolate with RNase treatment

SupramoleculeName: RESC5-tagged isolate with RNase treatment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: CTS-tagged RESC5 purified from RNase-treated mitochondrial extract by tandem affinity procedure
Source (natural)Organism: Trypanosoma brucei (eukaryote)

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Macromolecule #1: RNA-editing substrate-binding complex protein 1 (RESC1)

MacromoleculeName: RNA-editing substrate-binding complex protein 1 (RESC1)
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 52.60868 KDa
SequenceString: MLRLLRRSIV GSTFNIMVRR QNQGSVSQGA LNMRDQQAAA AENVTPERVW ALWNEGNLFS LSLAQLQGFL SRCGVRTDPA AKKAAVVRQ VEEYLHSKDT TVKGGGQGAA SPQQHQQHGQ QGGYGRWNQA SVMQPETLLD LSQAGFYEGA ANMVPKAFQL L VSDTAPDV ...String:
MLRLLRRSIV GSTFNIMVRR QNQGSVSQGA LNMRDQQAAA AENVTPERVW ALWNEGNLFS LSLAQLQGFL SRCGVRTDPA AKKAAVVRQ VEEYLHSKDT TVKGGGQGAA SPQQHQQHGQ QGGYGRWNQA SVMQPETLLD LSQAGFYEGA ANMVPKAFQL L VSDTAPDV VVSRVNTTAF PGFPSNTECY TLGASEKDVA IRSRYSKVLQ WCCLNMSNLQ MDGELYVDFG KLLLKPSVMR KN RRIVSSY TLQQRLQVNH PYTWVPTLPE SCLSKIQEQF LQPEGFAPIG KGVQLTYSGT IKRSKDQLHV DLDNKGKVLA VNS AWVNLQ TAWCTHAKGP DVRLLLRSRP PIRRQDVELF ASTPIIKLAD DDVADVLPPE HGQLVYLSED ETRLFERVSD RGVT ITVRE VKRQPLIILR DEEEDPRVEY SLSAHIPANA AKATDVRAVG LTAFELAGRL AGLVAEDFVR EYGCEAKL

UniProtKB: Guide RNA associated protein, GAP2

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Macromolecule #2: RNA-editing substrate-binding complex protein 2 (RESC2)

MacromoleculeName: RNA-editing substrate-binding complex protein 2 (RESC2)
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 55.526117 KDa
SequenceString: MLRARLKIFS ALNGATSAFS RAVAPLQIAT RQQSFSAAAP AASGDFSHIT RNTVWGLWNE GNLFSLSVPE LAFFLQEHCR VANVDPRAK KSALVRQVEE ILSAEQQASA TVPQEDNPHA IVVTDYDRAE DALEEADEYG DWGAEPGFED RRELDFMELS P GRMGERYD ...String:
MLRARLKIFS ALNGATSAFS RAVAPLQIAT RQQSFSAAAP AASGDFSHIT RNTVWGLWNE GNLFSLSVPE LAFFLQEHCR VANVDPRAK KSALVRQVEE ILSAEQQASA TVPQEDNPHA IVVTDYDRAE DALEEADEYG DWGAEPGFED RRELDFMELS P GRMGERYD PLSPRAFQLL HSETATDVGI ASIDPSKLPG QSKVKNALAA IHVAPNDANK MRFRMAFEWC LMNIWNMNMP GE LNIGAGK ALYYRSVAKQ NRNVMPLWTV QKHLYAQHPY AWFAIASESN VAAMESLAAA LNMSIQQERT TSYKVTIRRM AEF FDCELN GQLKCTMMNK PWDRFFVSHY IRSKMPDLRY VVRARHPIKK RIADAYLEAD ILRSTRDSVQ SVLSPELGDV VYCC ERVVR KWAKKTATGV TLQLVETKRT PLIITKAGDE GERLEYEWIV PLPQQAERID IAALTDELWE YGNKLAAALE EGMEE LMVH TMTAVSAY

UniProtKB: Mitochondrial guide RNA binding complex subunit 2

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Macromolecule #3: RNA-editing substrate-binding complex protein 3 (RESC3)

MacromoleculeName: RNA-editing substrate-binding complex protein 3 (RESC3)
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 53.146617 KDa
SequenceString: MSNPFEKVAR GIAFKMRSKV HKQGYSNTVM AQQARRLSPT GLLAMERLTE LTALQQRHQC TFDPALRSKA TQILRTLPLL SIDEDPYFT HTQRALRLAA YFGAVDLPVT YALINQHTKN AFMLDAFSMA SFFYTLAKLK HPQTKEIVGI LLPRLREVAP E LIAREAVH ...String:
MSNPFEKVAR GIAFKMRSKV HKQGYSNTVM AQQARRLSPT GLLAMERLTE LTALQQRHQC TFDPALRSKA TQILRTLPLL SIDEDPYFT HTQRALRLAA YFGAVDLPVT YALINQHTKN AFMLDAFSMA SFFYTLAKLK HPQTKEIVGI LLPRLREVAP E LIAREAVH ILRLLCSIQM ADAQLVKVVT ETVVATAADV PLRDARQCAF ILSETFPEEA QRILGAVEHR LCDDIDMNAD AN EVKTTIL DVCRVVSATC KGPRRLLNSV ARRSMELLPQ LTPLDVAFVL KAFHLSSYRH LRLLRVLSSS LAASFPTSNV TKE HGLAAS IVVQSLAHFY LSGCEEVVVT LVNASVNVLE GLNLALTLLA CVRLRCVSPG VDPAVDALCS GAPMRRYVHN AHSM QVTSR ILYGLAHAGR CRSDEEVAIV LPLLKSVVRT PGALRDDCRG FLLDAVTALG ADGECSNDAL QEQVRKVYER LSQDG GK

UniProtKB: Mitochondrial RNA binding protein

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Macromolecule #4: RNA-editing substrate-binding complex protein 4 (RESC4)

MacromoleculeName: RNA-editing substrate-binding complex protein 4 (RESC4)
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 120.847914 KDa
SequenceString: MNGRLYCLIR RITSPPVATR LIKEELCLSM AAIARLPLRR DQLAHVTNTE AITTRAQRIS HLCTPTELGM IAEGAEALSC NRFDLADAL IDGAYESVRR AASSTRLSHV SAIARYSASI KTYGNETITT LLKAGASLLQ KNDSVPVLKS FLGVAQSHLT D GEMRVLID ...String:
MNGRLYCLIR RITSPPVATR LIKEELCLSM AAIARLPLRR DQLAHVTNTE AITTRAQRIS HLCTPTELGM IAEGAEALSC NRFDLADAL IDGAYESVRR AASSTRLSHV SAIARYSASI KTYGNETITT LLKAGASLLQ KNDSVPVLKS FLGVAQSHLT D GEMRVLID EMCAKATEEQ RLCINSIGTQ SLAKDAAKCG EETLTKGNED GDETAVDDEE TQAWDMLRAR QWMLQLVRCG KP PTAAEAV QAMELYAHFA VRDFVLHEKI EDLVLLVLPT GNKFHLNEMH KIVLRSPNLF PRVRNTLGQD HSGVSDVHRA DRG VEWSDD PASSLTTTYT TSRAYSMLLL GQRLSEDIMF DVVQEQSETI PVDVAAQAAC LFAEKGDIPE GVILRLSAEL EHIS PQGVT AFVRAARRDS SGALLPHYAA VLNRFTERDL CDTPLETLLQ MCEVFALPAP RGTSEGDNDS INESQSKFQK ALIVR LFSV IQGSRDVPFL CKVAKAVRAF DANDELIQFV CSSICAQGAL SECEALIAFD MIRCCDFVYE PLLDAMEPVF RRLVES VSA MLEGKSTIND VEVRRCACFA TLQSEFDCPD FETLASLLVH TVEKNVTGCP VELIPSVGLL CVRTRRTSAL YIVGNKL EG NMQQLSDDAI GELARLLVGT ENLATKELAV EFQSVVVSRL LRQQSLPPDV VALSAVVWLR QGDKVGTIDE RSVDYIIK W MYAIGSSVYT DLCLAVHLSA SVESLSNALI DDLPRRLELL TTNEMANAIF GLGEVSDMGA RLSHQLVAER CSDYVVDHS QEFWSGKVIA RLLYGFSRMH CTKRSLYNVF ATRLAHRPVF SLLDQEAISF AIAAFGRVKY LDKKLFDRFT RWILDHSKDL NAAELLLTI RGVSRVMLLN DQLYDDLGSK AAEKVKEFPI ESQCVLLSSF GSLGVEHERL ASRMVSSIAE NREELTDATK A VDVITSLW SMNYDVEDDK HVAQLADWVV QRAEELTDES IGKLCLVLSD TNWRHVPLVR AIAEQSVRLQ GQQSISPKCC RE VLDVLGT FMIHHQGARE NLSALGRSIS KERIQLSEEE EQHLQLLLRR

UniProtKB: Mitochondrial RNA binding complex 1 subunit

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Macromolecule #5: RNA-editing substrate-binding complex protein 5 (RESC5)

MacromoleculeName: RNA-editing substrate-binding complex protein 5 (RESC5)
type: protein_or_peptide / ID: 5
Details: RESC5 is tagged in situ in Trypanosoma brucei (5691), which shared the same native environment as other RESC proteins.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 43.469484 KDa
SequenceString: MLRHTSRNNA LHAFVRSPHY RTIPSAGPNG IVVNRDMLVH QFRDFYKTLQ HCSLVDKVHL MSERPSVEAL RVADQMVSIG ATFLEMPLT GMEHRATEFM ESMRYVRGAG GPSTLASYLQ DTENCRCNSG DVVCLPNGIA VGHGPRTNAV AHTTLKQLFE V KDDQFSFD ...String:
MLRHTSRNNA LHAFVRSPHY RTIPSAGPNG IVVNRDMLVH QFRDFYKTLQ HCSLVDKVHL MSERPSVEAL RVADQMVSIG ATFLEMPLT GMEHRATEFM ESMRYVRGAG GPSTLASYLQ DTENCRCNSG DVVCLPNGIA VGHGPRTNAV AHTTLKQLFE V KDDQFSFD VFTLEQEGDA PPLGDYFGFA GSNVLLTWKD EHGLLAVDQY QQKQPHTEMN VVYLEPGCHF LSFYGVDHTI DV LVQKGYE RSMDSIAAAG LNPIPVQWSE MDKLGISMRA AVLPLKFFKA NVGGMLSRNK SRGARWQTHQ LQKGSGSGSA SSG ASAAGS SGASASSGAS AAGSSGASAG HHHHHHHHHH SGSEDQVDPR LIDGKASAWS HPQFEKGGGS GGGSGGSAWS HPQF EK

UniProtKB: Mitochondrial RNA binding protein

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Macromolecule #6: RNA-editing substrate-binding complex protein 6 (RESC6)

MacromoleculeName: RNA-editing substrate-binding complex protein 6 (RESC6)
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 57.823484 KDa
SequenceString: MRSALRRCIL RHQGCLRMKQ SLSAFPTVVT GMTRHQGNSL IGTTHGAELS LAGDPQSVSH LSARNIATEA LQMKKLHQER GGNPMLAQQ ARRVLFATSI AGQNLDARSV ALLLNTAVYF GMESDAKLVR ECIDYCLKND KLITVDVLPI VVTACATLKS R DAREVIEM ...String:
MRSALRRCIL RHQGCLRMKQ SLSAFPTVVT GMTRHQGNSL IGTTHGAELS LAGDPQSVSH LSARNIATEA LQMKKLHQER GGNPMLAQQ ARRVLFATSI AGQNLDARSV ALLLNTAVYF GMESDAKLVR ECIDYCLKND KLITVDVLPI VVTACATLKS R DAREVIEM QAQKAARNAK FLDAKDVTNI ISAFSKTGIN HEKLFAFLSR RVQTLARVGE FEAAHLVILA NAFSRLRYRD KF LFGAIAR RAMSLRERVT VNELVPLIVA FSKIGLKDPK LSKRFATKAM EYVDQMNAEQ VASMFMAFAY FGIRYDQLFG VLT NRAVEL IDEFNAQYIS TTLNAFQRIG INNPELFDNL AERALAVVQD HDARDISKTV TALAHFGLKD EELFKRLASH AASI ADQFD AMGLVNTAHA FARTNFLQQD MAVALSERSV YVCRLLDAGE TRRLLWALAK FQVRDPKILT PVFNRCLALH YDFFA DPTG SEEIEEIFDF YGPNFCPPLY QLYISRGSTP QA

UniProtKB: Guide RNA binding protein

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 290408
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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