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- PDB-6ybs: Structure of a human 48S translational initiation complex - head -

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Entry
Database: PDB / ID: 6ybs
TitleStructure of a human 48S translational initiation complex - head
Components
  • (40S ribosomal protein ...) x 13
  • (Eukaryotic translation initiation factor 3 subunit ...Eukaryotic initiation factor 3) x 2
  • 18S rRNA18S ribosomal RNA
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
KeywordsTRANSLATION / ribosome / initiation complex
Function / homology
Function and homology information


positive regulation of mRNA binding / viral translational termination-reinitiation / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / mRNA cap binding / formation of cytoplasmic translation initiation complex / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis ...positive regulation of mRNA binding / viral translational termination-reinitiation / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / mRNA cap binding / formation of cytoplasmic translation initiation complex / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / eukaryotic 48S preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / nucleolus organization / response to extracellular stimulus / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / NF-kappaB complex / negative regulation of phagocytosis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / pigmentation / protein kinase A binding / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / fibroblast growth factor binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / BH3 domain binding / Peptide chain elongation / Selenocysteine synthesis / monocyte chemotaxis / cysteine-type endopeptidase activator activity involved in apoptotic process / Formation of a pool of free 40S subunits / ribosomal small subunit export from nucleus / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of respiratory burst involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / gastrulation / spindle assembly / regulation of translational fidelity / MDM2/MDM4 family protein binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of smoothened signaling pathway / rescue of stalled ribosome / signaling adaptor activity / negative regulation of peptidyl-serine phosphorylation / maturation of SSU-rRNA / positive regulation of intrinsic apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of apoptotic signaling pathway / Maturation of protein E / positive regulation of microtubule polymerization / Maturation of protein E / positive regulation of JUN kinase activity / ER Quality Control Compartment (ERQC) / negative regulation of protein ubiquitination / translational initiation / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / DNA-(apurinic or apyrimidinic site) endonuclease activity / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / : / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S19e, conserved site ...Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / : / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S17e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / S25 ribosomal protein / Ribosomal protein S19A/S15e / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / 40S Ribosomal protein S10 / Ribosomal protein S28e conserved site / Ribosomal protein S28e / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S17e signature. / Ribosomal protein S28e / Ribosomal protein S28e signature. / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S14/S29 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Ubiquitin conserved site / Ubiquitin domain / RNA-binding domain superfamily / Ubiquitin domain signature. / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KH domain / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ubiquitin family / Ribosomal protein S13, conserved site / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S14 / Type-2 KH domain profile. / Ribosomal protein S13/S18 / Ubiquitin homologues / Ribosomal protein S19 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14p/S29e / Ribosomal protein S7 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S13-like, H2TH / Ubiquitin-like domain / Ribosomal protein S13 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S13 family profile. / Ribosomal protein S10p/S20e / Ribosomal protein S9 / Ribosomal protein S7p/S5e / Ribosomal protein S9/S16 / Ubiquitin domain profile. / Ribosomal protein S9 signature. / Zinc-binding ribosomal protein / Ribosomal protein S5 domain 2-type fold, subgroup / G-protein beta WD-40 repeat
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit G / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit G / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein RACK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBrito Querido, J. / Sokabe, M. / Kraatz, S. / Gordiyenko, Y. / Skehel, M. / Fraser, C. / Ramakrishnan, V.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Wellcome TrustWTY096570 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM092927 United States
CitationJournal: Science / Year: 2020
Title: Structure of a human 48 translational initiation complex.
Authors: Jailson Brito Querido / Masaaki Sokabe / Sebastian Kraatz / Yuliya Gordiyenko / J Mark Skehel / Christopher S Fraser / V Ramakrishnan /
Abstract: A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to ...A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48 initiation complex (i.e., the 48). The 48 then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48 The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43 The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40 subunit during scanning.
History
DepositionMar 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 2.0Dec 21, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_nat / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq
Item: _atom_site.label_seq_id / _chem_comp.formula ..._atom_site.label_seq_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.common_name / _entity_src_nat.pdbx_end_seq_num / _ndb_struct_na_base_pair.i_label_seq_id / _ndb_struct_na_base_pair.j_label_seq_id / _ndb_struct_na_base_pair_step.i_label_seq_id_1 / _ndb_struct_na_base_pair_step.i_label_seq_id_2 / _ndb_struct_na_base_pair_step.j_label_seq_id_1 / _ndb_struct_na_base_pair_step.j_label_seq_id_2 / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end

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Assembly

Deposited unit
x: Eukaryotic translation initiation factor 3 subunit D
c: Receptor of activated protein C kinase 1
n: 40S ribosomal protein S28
X: 40S ribosomal protein S17
h: 40S ribosomal protein S20
o: Eukaryotic translation initiation factor 3 subunit G
a: 40S ribosomal protein S10
m: 40S ribosomal protein S12
i: 40S ribosomal protein S29
b: 40S ribosomal protein S15
Z: 40S ribosomal protein S3
d: 40S ribosomal protein S19
e: 40S ribosomal protein S25
f: 40S ribosomal protein S18
V: 40S ribosomal protein S5
k: Ubiquitin-40S ribosomal protein S27a
Y: 40S ribosomal protein S16
A: 18S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)964,56348
Polymers963,79218
Non-polymers77030
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Eukaryotic translation initiation factor 3 subunit ... , 2 types, 2 molecules xo

#1: Protein Eukaryotic translation initiation factor 3 subunit D / Eukaryotic initiation factor 3 / eIF3d / Eukaryotic translation initiation factor 3 subunit 7 / eIF-3-zeta / eIF3 p66


Mass: 64060.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15371
#6: Protein Eukaryotic translation initiation factor 3 subunit G / Eukaryotic initiation factor 3 / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit ...eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit / Eukaryotic translation initiation factor 3 subunit 4 / eIF-3-delta / eIF3 p42 / eIF3 p44


Mass: 35662.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75821

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Protein , 2 types, 2 molecules ck

#2: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#16: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979

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40S ribosomal protein ... , 13 types, 13 molecules nXhamibZdefVY

#3: Protein 40S ribosomal protein S28 / / Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#4: Protein 40S ribosomal protein S17 / / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#5: Protein 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#7: Protein 40S ribosomal protein S10 / / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#8: Protein 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#9: Protein 40S ribosomal protein S29 / / Small ribosomal subunit protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#10: Protein 40S ribosomal protein S15 / / RIG protein / Small ribosomal subunit protein uS19


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#11: Protein 40S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#12: Protein 40S ribosomal protein S19 / / Small ribosomal subunit protein eS19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#13: Protein 40S ribosomal protein S25 / / Small ribosomal subunit protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#14: Protein 40S ribosomal protein S18 / / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#15: Protein 40S ribosomal protein S5 / / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#17: Protein 40S ribosomal protein S16 / / Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249

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RNA chain , 1 types, 1 molecules A

#18: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 603130.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Non-polymers , 2 types, 30 molecules

#19: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 48S initiation complex / Type: RIBOSOME / Entity ID: #1-#18 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 1 sec. / Electron dose: 107 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144882 / Symmetry type: POINT

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