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- EMDB-34212: Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-34212
TitleCryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome
Map data
Sample
  • Complex: Complex of BRCA1/BARD1 and H2AK127-UbcH5c-Ub nucleosome
    • Protein or peptide: Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-H
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
    • Protein or peptide: H2B
  • Protein or peptide: Breast cancer type 1 susceptibility protein
  • Protein or peptide: BRCA1-associated RING domain protein 1
  • Ligand: ZINC ION
Keywordsnucleosome / BRCA1/BARD1 / BRCA1 / BARD1 / H2AK127 / H2AK127-UbcH5c-Ub / NUCLEAR PROTEIN
Function / homology
Function and homology information


negative regulation of mRNA 3'-end processing / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / DNA Damage/Telomere Stress Induced Senescence / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function ...negative regulation of mRNA 3'-end processing / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / DNA Damage/Telomere Stress Induced Senescence / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / Recognition and association of DNA glycosylase with site containing an affected purine / Metalloprotease DUBs / Cleavage of the damaged purine / BRCA1-BARD1 complex / HDACs deacetylate histones / PRC2 methylates histones and DNA / BRCA1-C complex / UCH proteinases / BRCA1-B complex / BRCA1-A complex / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / negative regulation of centriole replication / sex-chromosome dosage compensation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / negative regulation of intracellular estrogen receptor signaling pathway / random inactivation of X chromosome / RMTs methylate histone arginines / nuclear ubiquitin ligase complex / ubiquitin-modified histone reader activity / chordate embryonic development / cellular response to indole-3-methanol / gamma-tubulin ring complex / negative regulation of fatty acid biosynthetic process / DNA strand resection involved in replication fork processing / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / homologous recombination / lateral element / tissue homeostasis / protein K6-linked ubiquitination / Ub-specific processing proteases / Impaired BRCA2 binding to PALB2 / regulation of phosphorylation / regulation of DNA damage checkpoint / XY body / mitotic G2/M transition checkpoint / negative regulation of protein export from nucleus / centrosome cycle / RNA polymerase binding / postreplication repair / DNA repair complex / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / intracellular membraneless organelle / HDR through Single Strand Annealing (SSA) / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / negative regulation of reactive oxygen species metabolic process / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / ubiquitin ligase complex / regulation of DNA repair / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / protein autoubiquitination / Meiotic synapsis / tubulin binding / male germ cell nucleus / positive regulation of DNA repair / cellular response to ionizing radiation / chromosome segregation / Nonhomologous End-Joining (NHEJ) / TP53 Regulates Transcription of DNA Repair Genes / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / negative regulation of cell growth / RING-type E3 ubiquitin transferase / Meiotic recombination / HDR through Homologous Recombination (HRR) / kinase binding / Metalloprotease DUBs / cytoplasmic ribonucleoprotein granule / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of protein catabolic process / positive regulation of angiogenesis / fatty acid biosynthetic process / ubiquitin-protein transferase activity / structural constituent of chromatin / p53 binding / UCH proteinases / KEAP1-NFE2L2 pathway / nucleosome / cellular response to tumor necrosis factor
Similarity search - Function
BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain ...BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Histone H3 signature 1. / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H4 / Histone H3 / Breast cancer type 1 susceptibility protein / Histone H2A type 1-H / BRCA1-associated RING domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsAi HS / Zebin T / Zhiheng D / Jiakun T / Liying Z / Jia-Bin L / Man P / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 81621002 and 21977090 China
CitationJournal: Chem / Year: 2023
Title: Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination.
Authors: Ai HS / Tong Z / Deng Z / Tian J / Zhang L / Sun M / Du Y / Xu Z / Shi Q / Liang L / Zheng Q / Li JB / Pan M / Liu L
History
DepositionSep 2, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34212.png

Downloads & links

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Map

FileDownload / File: emd_34212.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.018249646 - 0.037647523
Average (Standard dev.)0.000043581007 (±0.0017302328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34212_msk_1.map
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Additional map: #1

Fileemd_34212_additional_1.map
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Half map: #2

Fileemd_34212_half_map_1.map
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Half map: #1

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Sample components

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Entire : Complex of BRCA1/BARD1 and H2AK127-UbcH5c-Ub nucleosome

EntireName: Complex of BRCA1/BARD1 and H2AK127-UbcH5c-Ub nucleosome
Components
  • Complex: Complex of BRCA1/BARD1 and H2AK127-UbcH5c-Ub nucleosome
    • Protein or peptide: Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-H
    • DNA: DNA (147-MER)
    • DNA: DNA (147-MER)
    • Protein or peptide: H2B
  • Protein or peptide: Breast cancer type 1 susceptibility protein
  • Protein or peptide: BRCA1-associated RING domain protein 1
  • Ligand: ZINC ION

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Supramolecule #1: Complex of BRCA1/BARD1 and H2AK127-UbcH5c-Ub nucleosome

SupramoleculeName: Complex of BRCA1/BARD1 and H2AK127-UbcH5c-Ub nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #9, #1-#3, #5-#6, #4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.530447 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAS EAYLVGLFED TNLSAIHAKR VTIMPKDIQ LARRIRGER

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.123692 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LRDNIQGITK PAIRRLARRG GVKRISGLIY EETRGVLKVF LENVIRDAVT YTEHAKRKTV TAMDVVYALK RQGRTLYGFG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-H

MacromoleculeName: Histone H2A type 1-H / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.066128 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLG RVTIAQGGVL PNIQAVLLPK K

UniProtKB: Histone H2A type 1-H

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Macromolecule #4: H2B

MacromoleculeName: H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.937998 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTSARSRKE SYSVYVYKVL KQVHPDTGIS SKAMGIMNSF VNDIFERIAG EASRLAHYNK RSTITSREIQ T AVRLLLPG ELAKHAVSEG TKAVTKYTSA

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Macromolecule #7: Breast cancer type 1 susceptibility protein

MacromoleculeName: Breast cancer type 1 susceptibility protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.626693 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LRVEEVQNVI NAMQKILECP ICLELIKEPV STKCDHIFCK FCMLKLLNQK KGPSQCPLCK NDITKRSLQE STRFSQLVEE LLKIICAFQ LDT

UniProtKB: Breast cancer type 1 susceptibility protein

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Macromolecule #8: BRCA1-associated RING domain protein 1

MacromoleculeName: BRCA1-associated RING domain protein 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.348078 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEPDGRGAWA HSRAALDRLE KLLRCSRCTN ILREPVCLGG CEHIFCSNCV SDCIGTGCPV CYTPAWIQDL KINRQLDSMI QLCSKLRNL LHD

UniProtKB: BRCA1-associated RING domain protein 1

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Macromolecule #9: Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isofo...

MacromoleculeName: Ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast), isoform CRA_a
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.657938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALKRINKEL SDLARDPPAQ SSAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDIL RSQWSPALTI SKVLLSISSL LSDPNPDDPL VPEIARIYKT DRDKYNRISR EWTQKYAM

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Macromolecule #5: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.604047 KDa
SequenceString: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String:
(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DC)(DA)(DG)

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Macromolecule #6: DNA (147-MER)

MacromoleculeName: DNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.145754 KDa
SequenceString: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String:
(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT)

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68006
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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