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- PDB-3bt2: Structure of urokinase receptor, urokinase and vitronectin complex -

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Basic information

Entry
Database: PDB / ID: 3bt2
TitleStructure of urokinase receptor, urokinase and vitronectin complex
Components
  • (anti-uPAR antibody, ...) x 2
  • Urokinase plasminogen activator surface receptor
  • Urokinase-type plasminogen activator
  • Vitronectin
KeywordsIMMUNE SYSTEM / protein-protein interaction / Glycoprotein / GPI-anchor / Lipoprotein / Membrane / Receptor / Secreted / Blood coagulation / EGF-like domain / Fibrinolysis / Hydrolase / Kringle / Phosphoprotein / Plasminogen activation / Protease / Serine protease / Zymogen / Cell adhesion / Heparin-binding / Sulfation / Immunoglobulin domain
Function / homology
Function and homology information


urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / smooth muscle cell-matrix adhesion / rough endoplasmic reticulum lumen / peptidase inhibitor complex / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / positive regulation of homotypic cell-cell adhesion / urokinase plasminogen activator signaling pathway / alphav-beta3 integrin-vitronectin complex ...urokinase plasminogen activator receptor activity / Attachment of GPI anchor to uPAR / smooth muscle cell-matrix adhesion / rough endoplasmic reticulum lumen / peptidase inhibitor complex / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / positive regulation of homotypic cell-cell adhesion / urokinase plasminogen activator signaling pathway / alphav-beta3 integrin-vitronectin complex / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / regulation of signaling receptor activity / negative regulation of plasminogen activation / positive regulation of vascular endothelial growth factor signaling pathway / serine-type endopeptidase complex / regulation of smooth muscle cell migration / Dissolution of Fibrin Clot / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / extrinsic component of membrane / extracellular matrix structural constituent / positive regulation of smooth muscle cell migration / scavenger receptor activity / smooth muscle cell migration / Molecules associated with elastic fibres / positive regulation of DNA binding / plasminogen activation / positive regulation of epidermal growth factor receptor signaling pathway / Syndecan interactions / cell adhesion mediated by integrin / positive regulation of wound healing / regulation of cell adhesion mediated by integrin / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of release of cytochrome c from mitochondria / endodermal cell differentiation / polysaccharide binding / oligodendrocyte differentiation / regulation of proteolysis / basement membrane / tertiary granule membrane / negative regulation of blood coagulation / protein polymerization / negative regulation of fibrinolysis / ECM proteoglycans / Integrin cell surface interactions / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / collagen binding / negative regulation of proteolysis / extracellular matrix organization / liver regeneration / Regulation of Complement cascade / cell-matrix adhesion / integrin-mediated signaling pathway / cell projection / positive regulation of receptor-mediated endocytosis / Golgi lumen / integrin binding / positive regulation of protein phosphorylation / chemotaxis / blood coagulation / cell migration / signaling receptor activity / heparin binding / regulation of cell population proliferation / : / blood microparticle / response to hypoxia / cell adhesion / immune response / positive regulation of cell migration / endoplasmic reticulum lumen / signaling receptor binding / protein domain specific binding / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / endoplasmic reticulum / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / CD59 antigen, conserved site / Ly-6 / u-PAR domain signature. / u-PAR/Ly-6 domain / Ly-6 antigen / uPA receptor -like domain / Ly-6 antigen/uPA receptor-like / Plasminogen Kringle 4 / Plasminogen Kringle 4 / CD59 / CD59 ...: / CD59 antigen, conserved site / Ly-6 / u-PAR domain signature. / u-PAR/Ly-6 domain / Ly-6 antigen / uPA receptor -like domain / Ly-6 antigen/uPA receptor-like / Plasminogen Kringle 4 / Plasminogen Kringle 4 / CD59 / CD59 / Somatomedin B domain, chordata / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Snake toxin-like superfamily / Laminin / Laminin / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Urokinase-type plasminogen activator / Vitronectin / Urokinase plasminogen activator surface receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuang, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Crystal structures of two human vitronectin, urokinase and urokinase receptor complexes
Authors: Huai, Q. / Zhou, A. / Lin, L. / Mazar, A.P. / Parry, G.C. / Callahan, J. / Shaw, D.E. / Furie, B. / Furie, B.C. / Huang, M.
History
DepositionDec 27, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urokinase-type plasminogen activator
B: Vitronectin
L: anti-uPAR antibody, light chain
H: anti-uPAR antibody, heavy chain
U: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9158
Polymers97,8455
Non-polymers1,0703
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Urokinase-type plasminogen activator
L: anti-uPAR antibody, light chain
H: anti-uPAR antibody, heavy chain
U: Urokinase plasminogen activator surface receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3427
Polymers93,2724
Non-polymers1,0703
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-17.3 kcal/mol
Surface area38680 Å2
MethodPISA
3
B: Vitronectin


Theoretical massNumber of molelcules
Total (without water)4,5731
Polymers4,5731
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.096, 87.205, 124.274
Angle α, β, γ (deg.)90.00, 94.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AU

#1: Protein Urokinase-type plasminogen activator / uPA / U-plasminogen activator


Mass: 15359.318 Da / Num. of mol.: 1
Fragment: urokinase amino terminal fragment, Urokinase-type plasminogen activator long chain A, UNP residues 21-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU / Plasmid: pMT/Bip / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00749
#5: Protein Urokinase plasminogen activator surface receptor / uPAR / U-PAR / Monocyte activation antigen Mo3 / CD87 antigen


Mass: 31601.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAUR, MO3, UPAR / Plasmid: pMT/Bip / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells / References: UniProt: Q03405

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Antibody , 2 types, 2 molecules LH

#3: Antibody anti-uPAR antibody, light chain


Mass: 23269.691 Da / Num. of mol.: 1 / Fragment: Fab fragment, light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Antibody anti-uPAR antibody, heavy chain


Mass: 23041.734 Da / Num. of mol.: 1 / Fragment: Fab fragment, heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Protein/peptide / Non-polymers , 2 types, 58 molecules B

#2: Protein/peptide Vitronectin / Serum-spreading factor / S-protein / V75


Mass: 4573.103 Da / Num. of mol.: 1 / Fragment: sometomedin-B domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VTN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04004
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 3 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has protein modificationY
Sequence detailsTHIS COORDINATES IN CHAINS L AND H ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. IT IS DUE TO KABAT-WU ...THIS COORDINATES IN CHAINS L AND H ARE USED NON-SEQUENTIAL RESIDUE NUMBERING. IT IS DUE TO KABAT-WU NUMBERING, WHICH IS TYPICAL FOR ANTIBODY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 295 K / Method: microdialysis / pH: 7.5
Details: 8% PEG 4000, 2.5% ethanol, 0.05% sodium azide, 50mM cacodylate pH 6.5, pH 7.5, MICRODIALYSIS, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11
SYNCHROTRONNSLS X12C21
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
ADSC QUANTUM 2102CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 38381 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 24.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3675 / Rsym value: 0.356 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2fd6

2fd6


Resolution: 2.5→42.88 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.878 / SU B: 28.105 / SU ML: 0.316 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.463 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 1191 3.1 %RANDOM
Rwork0.22862 ---
obs0.22993 37032 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 62.232 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0.7 Å2
2--1.5 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6527 0 70 57 6654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0216782
X-RAY DIFFRACTIONr_bond_other_d0.0030.024587
X-RAY DIFFRACTIONr_angle_refined_deg1.741.959213
X-RAY DIFFRACTIONr_angle_other_deg1.113.0111097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8485835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00124.403293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.315151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.281531
X-RAY DIFFRACTIONr_chiral_restr0.1220.21003
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027496
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021321
X-RAY DIFFRACTIONr_nbd_refined0.2270.21296
X-RAY DIFFRACTIONr_nbd_other0.2130.24541
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23036
X-RAY DIFFRACTIONr_nbtor_other0.0960.23667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.2181
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.4170.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0391.55317
X-RAY DIFFRACTIONr_mcbond_other0.1661.51721
X-RAY DIFFRACTIONr_mcangle_it1.26426778
X-RAY DIFFRACTIONr_scbond_it2.00133050
X-RAY DIFFRACTIONr_scangle_it2.9264.52435
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 81 -
Rwork0.267 2593 -
obs--94.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
115.7256-0.4411-4.695926.5061-3.43397.8644-0.77671.8843-0.772-1.96150.3062-3.74082.56481.00520.47050.43890.1835-0.01990.88-0.10260.222754.035-46.90642.143
29.8112-1.2009-1.65178.70125.11444.67450.51810.24170.89-0.367-0.3248-1.2106-0.68660.8789-0.19340.0711-0.0007-0.00290.0780.4202-0.284151.284-40.54178.763
36.14472.01340.34475.9408-2.66436.0103-0.091-0.1513-0.19660.19040.0273-0.0426-0.06070.20140.0637-0.03820.0749-0.113-0.19340.2814-0.551732.485-38.1460.387
40.71950.02870.33081.7667-1.42492.1140.0931-0.07070.15540.1367-0.2159-0.01530.01240.22260.1228-0.4237-0.02470.0117-0.3873-0.0373-0.444318.81-7.06718.951
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BB2 - 411 - 40
2X-RAY DIFFRACTION2AA41 - 13243 - 134
3X-RAY DIFFRACTION3UE1 - 803 - 82
4X-RAY DIFFRACTION3AA9 - 4011 - 42
5X-RAY DIFFRACTION4LC1 - 2121 - 211
6X-RAY DIFFRACTION4HD1 - 2081 - 213
7X-RAY DIFFRACTION4UE87 - 18589 - 187
8X-RAY DIFFRACTION4UE186 - 275188 - 277

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