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- PDB-1he8: Ras G12V - PI 3-kinase gamma complex -

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Basic information

Entry
Database: PDB / ID: 1he8
TitleRas G12V - PI 3-kinase gamma complex
Components
  • PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT, GAMMA ISOFORM
  • TRANSFORMING PROTEIN P21/H-RAS-1
KeywordsKINASE/HYDROLASE / COMPLEX (PHOSPHOINOSITIDE KINASE-RAS) / PHOSPHOINOSITIDE 3-KINASE GAMMA - H-RAS G12V COMPLEX / PHOSPHATIDYLINOSITOL 3-KINASE / PI3K / PI 3-K / PI 3-KINASE / SECOND MESSENGER GENERATION / RAS EFFECTOR / H-RAS G12V / ONCOGENE PROTEIN / GMPPNP / GTP / RAS-BINDING DOMAIN / HEAT DOMAIN / KINASE-HYDROLASE complex
Function / homology
Function and homology information


negative regulation of triglyceride catabolic process / secretory granule localization / natural killer cell chemotaxis / neutrophil extravasation / phosphatidylinositol-4-phosphate 3-kinase / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / regulation of calcium ion transmembrane transport / T cell chemotaxis ...negative regulation of triglyceride catabolic process / secretory granule localization / natural killer cell chemotaxis / neutrophil extravasation / phosphatidylinositol-4-phosphate 3-kinase / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / regulation of calcium ion transmembrane transport / T cell chemotaxis / phospholipase C activator activity / negative regulation of fibroblast apoptotic process / phosphatidylinositol 3-kinase complex, class IB / GTPase complex / sphingosine-1-phosphate receptor signaling pathway / phosphatidylinositol 3-kinase complex, class IA / oncogene-induced cell senescence / positive regulation of ruffle assembly / dendritic cell chemotaxis / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / negative regulation of GTPase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / positive regulation of miRNA metabolic process / phosphatidylinositol 3-kinase / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / phosphatidylinositol-3-phosphate biosynthetic process / T-helper 1 type immune response / 1-phosphatidylinositol-3-kinase activity / positive regulation of wound healing / mast cell degranulation / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hepatocyte apoptotic process / defense response to protozoan / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / regulation of cell adhesion mediated by integrin / phosphatidylinositol-mediated signaling / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / regulation of angiogenesis / adipose tissue development / SHC-mediated cascade:FGFR2 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / phosphorylation / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR2 signaling / T cell proliferation / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / cellular response to cAMP / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / GPVI-mediated activation cascade / Tie2 Signaling / FRS-mediated FGFR1 signaling / GRB2 events in EGFR signaling / FLT3 Signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / EPHB-mediated forward signaling / neutrophil chemotaxis / Signaling by FGFR1 in disease / myelination / ephrin receptor binding / GRB2 events in ERBB2 signaling / intrinsic apoptotic signaling pathway / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of endothelial cell migration / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade
Similarity search - Function
PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase, accessory domain (PIK) / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / C2 domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. ...PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase, accessory domain (PIK) / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / C2 domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Small GTPase, Ras-type / small GTPase Ras family profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Alpha Horseshoe / Small GTP-binding protein domain / Armadillo-type fold / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas / GTPase HRas / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPacold, M.E. / Suire, S. / Perisic, O. / Lara-Gonzalez, S. / Davis, C.T. / Hawkins, P.T. / Walker, E.H. / Stephens, L. / Eccleston, J.F. / Williams, R.L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Crystal Structure and Functional Analysis of Ras Binding to its Effector Phosphoinositide 3-Kinase Gamma
Authors: Pacold, M.E. / Suire, S. / Perisic, O. / Lara-Gonzalez, S. / Davis, C.T. / Walker, E.H. / Hawkins, P.T. / Stephens, L. / Eccleston, J.F. / Williams, R.L.
History
DepositionNov 20, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT, GAMMA ISOFORM
B: TRANSFORMING PROTEIN P21/H-RAS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,0914
Polymers129,5442
Non-polymers5472
Water1086
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-5.2 kcal/mol
Surface area48480 Å2
MethodPQS
Unit cell
Length a, b, c (Å)113.635, 113.635, 183.881
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsHETERODIMER OF A 101 KDA SUBUNIT AND A 120 KDA CATALYTICSUBUNIT

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Components

#1: Protein PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT, GAMMA ISOFORM / PI3-KINASE P110 SUBUNIT GAMMA / PTDINS-3-KINASE P110 / PI3K


Mass: 110626.953 Da / Num. of mol.: 1 / Fragment: P110 GAMMA CATALYTIC SUBUNIT / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVL1393 / Cell line (production host): Sf9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P48736, phosphatidylinositol 3-kinase
#2: Protein TRANSFORMING PROTEIN P21/H-RAS-1 / C-H-RAS / H-RAS


Mass: 18917.271 Da / Num. of mol.: 1 / Fragment: EFFECTOR DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-11A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P23175, UniProt: P01112*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A: PHOSPHATIDYLINOSITOL 3-KINASE, 3-PHOSPHORYLATES THE CELLULAR PHOSPHOINOSITIDE PTDINS-4,5- ...CHAIN A: PHOSPHATIDYLINOSITOL 3-KINASE, 3-PHOSPHORYLATES THE CELLULAR PHOSPHOINOSITIDE PTDINS-4,5-BIPHOSPHATE (PTDINS(4,5)P2) BY THE REACTION, ATP + 1-PHOSPHATIDYL-1D-MYO-INOSITOL = ADP + 1-PHOSPHATIDYL-1D-MYO-INOSITOL 3-PHOSPHATE THE ENZYME IS ACTIVATED BY BOTH THE ALPHA AND THE BETA-GAMMA G PROTEINS. THE PROTEIN HAS THE MUTATIONS V223K, V327A CHAIN B: H-RAS, BELONGS TO THE SMALL GTPASE SUPERFAMILY OF PROTEINS INVOLVED IN ENZYME REGULATION ACTIVATED BY A GUANINE NUCLEOTIDE-EXCHANGE FACTOR (GEF) AND INACTIVATED BY A GTPASE- ACTIVATING PROTEIN (GAP). THE PROTEIN HAS THE MUTATION G12V.
Sequence detailsCHAIN A, P48736: IN THE STRUCTURE, A528-A619 IN THE HELICAL DOMAIN WAS PROBABLY LOST TO PROTEOLYSIS ...CHAIN A, P48736: IN THE STRUCTURE, A528-A619 IN THE HELICAL DOMAIN WAS PROBABLY LOST TO PROTEOLYSIS DURING CRYSTALLIZATION AND IS NOT VISIBLE IN THE DENSITY. THE SEQUENCE IN THE DATABASE CONTAINS AN ERROR. THE ACTUAL LENGTH OF THE ENZYME IS 1102 RESIDUES, NOT 1101 AS IN SWS ENTRY P48736, DUE TO INSERTION OF AN ALA FOLLOWING ALA-29. RESIDUES 1103 TO 1108 ARE THE C-TERMINAL HIS TAG CHAIN B, P23175: THE RAS CONSTRUCT USED FOR CRYSTALLIZATION CONTAINED ONLY THE FIRST 166 RESIDUES OF H-RAS G12V.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 64 %
Crystal growpH: 6.3 / Details: 50 MM KH2PO4 PH 6.3, 4.3% PEG 8000
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.170 mMH-Ras1drop
20.029 mMPI3K1drop
350 mMpotassium phosphate1reservoirpH6.3
44.3 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2000 / Details: GE(220) AND MULTILAYER
RadiationMonochromator: DIAMOND C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 25822 / % possible obs: 91.6 % / Redundancy: 9 % / Biso Wilson estimate: 82.3 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 20
Reflection shellResolution: 3→3.19 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 1.7 / % possible all: 50.5
Reflection
*PLUS
Num. measured all: 232825
Reflection shell
*PLUS
% possible obs: 50.5 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1E8Y AND 5P21

1e8y

5p21


Resolution: 3→52.03 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2257126.69 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 1085 - 1108 ARE NOT VISIBLE IN THE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1510 5.9 %RANDOM
Rwork0.212 ---
obs0.212 25783 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.7474 Å2 / ksol: 0.384614 e/Å3
Displacement parametersBiso mean: 70.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.67 Å221.15 Å20 Å2
2--4.67 Å20 Å2
3----9.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3→52.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7395 0 33 6 7434
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.404 158 6.3 %
Rwork0.339 2362 -
obs--54.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4GNP.PARGNP.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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