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- PDB-7p56: Variant Surface Glycoprotein 2 (VSG2, MiTat1.2, VSG221) Bound to ... -

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Basic information

Entry
Database: PDB / ID: 7p56
TitleVariant Surface Glycoprotein 2 (VSG2, MiTat1.2, VSG221) Bound to Calcium
ComponentsVariant surface glycoprotein MITAT 1.2
KeywordsMEMBRANE PROTEIN / Variant Surface Glycoprotein / VSG Coat / Trypanosoma brucei / Immune Evasion / African trypanosome / calcium / metal binding
Function / homologyVariant surface glycoprotein C-terminal domain superfamily / Trypanosome variant surface glycoprotein, A-type, N-terminal domain / Trypanosome variant surface glycoprotein (A-type) / evasion of host immune response / side of membrane / plasma membrane / Variant surface glycoprotein MITAT 1.2
Function and homology information
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.735 Å
AuthorsGkeka, A. / Aresta-Branco, F. / Stebbins, C.E. / Papavasiliou, F.N.
Citation
Journal: Cell Rep / Year: 2023
Title: Immunodominant surface epitopes power immune evasion in the African trypanosome.
Authors: Gkeka, A. / Aresta-Branco, F. / Triller, G. / Vlachou, E.P. / van Straaten, M. / Lilic, M. / Olinares, P.D.B. / Perez, K. / Chait, B.T. / Blatnik, R. / Ruppert, T. / Verdi, J.P. / Stebbins, ...Authors: Gkeka, A. / Aresta-Branco, F. / Triller, G. / Vlachou, E.P. / van Straaten, M. / Lilic, M. / Olinares, P.D.B. / Perez, K. / Chait, B.T. / Blatnik, R. / Ruppert, T. / Verdi, J.P. / Stebbins, C.E. / Papavasiliou, F.N.
#1: Journal: Biorxiv / Year: 2022
Title: Immunodominant surface epitopes power immune evasion in the African trypanosome
Authors: Gkeka, A. / Aresta-Branco, F. / Triller, G. / Vlachou, E.P. / Lilic, M. / Olinares, P.D.B. / Perez, K. / Chait, B.T. / Blatnik, R. / Ruppert, T. / Stebbins, C.E. / Papavasiliou, F.N.
History
DepositionJul 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 5, 2023Group: Database references / Category: citation / citation_author
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Variant surface glycoprotein MITAT 1.2
B: Variant surface glycoprotein MITAT 1.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6206
Polymers102,2052
Non-polymers1,4154
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-34 kcal/mol
Surface area24760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.915, 87.585, 88.121
Angle α, β, γ (deg.)90.000, 98.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Variant surface glycoprotein MITAT 1.2 / VSG 221


Mass: 51102.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: VSG2 WT binds calcium. / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Production host: Trypanosoma brucei brucei (eukaryote) / References: UniProt: P26332
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M K-acetate, 22% PEG8000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.735→61.81 Å / Num. obs: 65518 / % possible obs: 97.26 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07673 / Rpim(I) all: 0.04939 / Rrim(I) all: 0.07673 / Net I/σ(I): 10.93
Reflection shellResolution: 1.735→1.797 Å / Rmerge(I) obs: 1.565 / Mean I/σ(I) obs: 0.75 / Num. unique obs: 5809 / CC1/2: 0.307 / Rpim(I) all: 1.032 / Rrim(I) all: 1.882 / % possible all: 86.82

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSVERSION Oct 15, 2015 BUILT=20151015data reduction
XDSVERSION Oct 15, 2015 BUILT=20151015data scaling
PHENIXPHENIX: Phaser 2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VSG

1vsg


Resolution: 1.735→61.81 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 3206 4.94 %
Rwork0.1894 61737 -
obs0.1911 65518 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.64 Å2 / Biso mean: 34.7901 Å2 / Biso min: 16.46 Å2
Refinement stepCycle: final / Resolution: 1.735→61.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 91 341 5360
Biso mean--46.47 39.65 -
Num. residues----680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.73-1.760.4091210.36431977209873
1.76-1.790.35051390.36912726286597
1.79-1.820.37481340.36322626276096
1.82-1.850.35221360.33012733286999
1.85-1.880.34591450.29612724286999
1.88-1.920.33141280.29182695282398
1.92-1.960.30121450.26572748289399
1.96-20.28681430.24192706284999
2-2.050.28961110.23772758286999
2.05-2.10.30391290.22822653278298
2.1-2.150.23431290.21982765289499
2.15-2.220.27971380.21392642278097
2.22-2.290.25371480.20172697284598
2.29-2.370.23291590.18042740289999
2.37-2.470.21131480.17322696284499
2.47-2.580.24081480.1762754290299
2.58-2.710.21711360.17292741287799
2.71-2.890.19941210.17222729285098
2.89-3.110.20661390.16712722286199
3.11-3.420.21851400.16242741288199
3.42-3.920.18071550.152701285697
3.92-4.930.16491570.15282716287398
4.93-87.230.1951570.19012747290498
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)
12.5723-4.1136-1.48058.08092.74281.01540.07630.21810.0236-0.0717-0.15990.07260.0406-0.13480.07430.2593-0.0182-0.01220.27830.03390.2148-67.103102.5702108.8765
24.2144-3.3396-2.8178.93266.52256.00730.20630.2280.0831-0.2577-0.0133-0.2349-0.20990.1105-0.18730.2868-0.0270.0450.2887-0.0310.1827-46.552271.386788.4387
32.9486-0.30942.299.60461.89612.26220.41380.7914-0.4102-1.1827-0.0987-1.79630.53821.6852-0.17620.38230.10950.09820.7155-0.13880.5224-33.797965.227478.772
44.2089-1.3859-4.54054.19844.19599.2044-0.11850.18420.1772-0.06120.5605-0.47110.04810.6643-0.46390.226-0.03350.03810.3154-0.08440.3082-41.155775.405395.4939
58.3642-5.6746-6.98918.22598.61319.6627-0.10440.50270.23620.26170.1675-0.31120.24390.1734-0.08940.3207-0.04080.03640.2761-0.00540.2823-49.666685.9418108.4671
63.6956-2.9988-0.27373.55080.76520.95750.09480.2701-0.0233-0.1965-0.21550.2155-0.0831-0.19490.12480.1765-0.0176-0.00750.19430.00740.1927-74.9824105.28114.3058
76.9795-6.0653-6.69445.34266.0236.99690.39451.0876-0.4552-0.8816-0.50710.69010.182-1.03920.13040.2748-0.039-0.07310.33140.01790.319-73.426195.1598109.8095
88.38080.1899-7.04543.54470.03586.3976-0.1990.12370.5616-0.1431-0.0470.07820.2128-0.24930.28830.36060.0102-0.04770.3562-0.01310.2685-64.546290.3362101.2255
93.39932.51381.22556.84890.06978.9066-0.16850.11790.1615-0.40790.07630.1231-0.1015-0.18610.09290.1961-0.00110.02930.22190.03340.2304-58.2113105.6583105.6297
102.0953-0.7536-0.62642.03750.54383.3082-0.01410.05240.2642-0.0276-0.004-0.01-0.3438-0.00020.00430.2442-0.0113-0.03750.1675-0.00440.2472-69.9448116.736124.0762
114.4532.2704-0.41655.786-0.61025.737-0.0107-0.1361-0.00020.0115-0.082-0.4581-0.08640.4340.09360.1338-0.0111-0.00350.1854-0.00330.2034-53.7482105.0273116.4253
127.7888-5.9128-6.28057.67355.18765.2838-0.07690.38260.0707-0.56270.2513-0.83260.10920.0971-0.13320.329-0.04780.10170.27930.00010.3238-48.587592.3725103.4591
137.69-2.7251-4.290.99841.32474.16940.11480.43480.7995-0.7360.2794-0.9382-1.17980.5708-0.52560.6117-0.16750.22170.4284-0.05890.5068-40.333684.525690.5767
140.1257-0.32170.29361.4619-0.26411.0568-0.0367-0.18030.0587-0.04610.1636-0.7539-0.0910.4115-0.11980.3571-0.41140.17990.7458-0.38630.6259-31.587278.808889.8047
151.43510.8965-0.21920.9516-0.63560.6610.037-0.91810.46080.01570.4655-1.221-0.13221.1082-0.3830.31420.02330.04980.9152-0.49710.8117-25.420370.007691.0493
161.8674-1.5171-2.73311.23282.31129.36810.1948-0.16360.2903-0.44270.0998-0.443-0.26431.0709-0.34310.8238-0.34230.37920.9864-0.39050.499-24.906974.856581.7221
175.08231.9136-0.8283.4979-0.05712.42540.0451-0.10810.5992-0.49180.1778-0.0637-0.61250.5198-0.22810.4816-0.13430.15580.4984-0.13120.2871-41.163771.891478.7229
189.70747.11566.67745.23434.87884.607-0.15010.07060.7401-0.5334-0.72251.2803-1.1657-1.12710.83420.53280.093-0.00230.5116-0.14810.4598-55.416468.352378.0883
193.01012.70852.21139.6161-5.01088.44880.0736-0.19910.5642-0.4237-0.31190.2844-0.669-1.36030.12810.40750.02040.05650.432-0.08990.2991-54.763769.335288.2091
206.8933-1.8562.6266.8827-4.45218.52240.27810.4063-0.72760.22220.1329-0.43730.89160.4855-0.3910.4165-0.012-0.06520.3636-0.14710.3439-46.52557.586.7333
212.9195-2.3661-3.34962.27963.16374.23140.0088-0.04660.01590.11110.0166-0.05460.07350.0448-0.01420.3068-0.0193-0.00910.20720.0210.2403-65.284188.2671127.2735
226.9777-2.445-1.70945.02252.03645.48720.11140.0706-0.37530.32070.1478-0.44150.65790.6295-0.22730.28450.0431-0.02660.26-0.06960.2442-43.206663.3409102.2218
237.19813.1393-2.7955.44630.10991.517-0.55550.3989-1.0431-0.41290.3521-0.81671.01330.4790.1090.8540.3735-0.03960.6047-0.32340.597-37.519950.105594.2814
244.499-3.0117-2.35525.10183.29673.51520.12660.5307-0.62590.0209-0.27920.29910.479-0.05440.15850.40660.0119-0.0280.2932-0.09110.2558-50.102160.563898.4354
254.07982.5171-3.44538.4941-6.10545.20380.3132-0.00390.18390.27680.1740.5597-0.7197-0.5572-0.51430.32260.01710.01520.2963-0.01310.2587-59.0675.7104101.4903
260.9161-0.7921-0.91471.7712.36394.8675-0.0472-0.02620.0360.23970.0139-0.03280.1454-0.00310.03230.2085-0.0309-0.01030.17480.02970.199-67.509396.0352128.0569
271.2924-0.20441.87713.6066-1.62298.03580.070.0191-0.17160.02650.0932-0.45930.14270.7866-0.13440.28610.0232-0.05820.3121-0.04570.3162-59.835995.0991133.6879
284.7068-0.3324-2.67057.7979-1.05744.08710.0099-0.169-0.06350.13980.0251-0.51560.28270.1658-0.02420.27930.0221-0.04950.2759-0.01290.2133-54.701283.95121.8694
294.04531.815-0.35764.6691.14034.7933-0.25020.0446-0.43570.20190.27250.12530.7054-0.1477-0.04420.3686-0.02510.03920.17430.00920.301-69.35679.0598126.988
301.9251-1.8136-2.78559.20346.63377.1119-0.06470.0353-0.10310.7629-0.30830.36580.6122-0.41490.46330.3269-0.04450.04170.25790.03980.2867-80.092789.1567135.8597
313.4025-3.28162.84027.0451-5.81688.4763-0.1828-0.3146-0.0110.67330.18950.2122-0.5961-0.60510.02850.2572-0.00020.0280.2218-0.04420.2061-82.1411108.6672134.6583
321.3449-0.4010.48382.185-0.15810.1777-0.01070.01180.06380.0304-0.04260.05260.0616-0.11250.05210.2280.0050.00560.2647-0.01330.241-83.1828100.2132126.6427
338.9514-6.8705-9.15588.20547.6439.7310.17150.7096-0.34190.3374-0.81740.66230.2045-0.99790.6330.1825-0.04140.01230.3033-0.00970.2434-82.96291.9938130.0976
346.7591-2.4389-2.32057.3859-3.81977.48910.1420.2347-0.1565-0.65390.00340.58510.5582-0.8101-0.13580.1964-0.0686-0.00970.2359-0.05160.2464-77.59884.7784118.793
355.0951-5.5274-4.20785.9094.52853.7427-0.12920.0532-0.29390.3007-0.02550.29690.2593-0.06270.17230.4087-0.0335-0.0250.2584-0.01330.2984-60.93568.5966111.6101
366.5133-0.4861-5.85824.24061.12495.8474-0.37140.73110.00090.4184-0.11530.24721.3142-1.15860.49960.52-0.1146-0.0170.3995-0.09140.3268-56.130652.878796.1713
375.23570.7750.50350.12750.32115.75670.22870.2338-1.4239-0.7344-0.1062-0.1682.06890.0535-0.16981.13940.0177-0.0250.4033-0.14070.5692-50.244245.052196.0866
386.71123.0212-0.1712.44991.17442.6322-0.0643-0.4815-0.71840.55820.2166-0.68570.88070.3467-0.12580.88070.2315-0.14120.3622-0.09530.5631-42.092851.8617105.6999
397.4381-4.86846.14676.5662-7.66949.5713-0.0266-0.477-0.26550.96340.3007-0.4466-0.05180.6856-0.22370.47860.1008-0.08550.5572-0.22280.4925-36.148764.0514106.8931
407.6439-0.4542-1.62173.2168-1.86791.56150.0430.3005-0.3343-0.10350.5406-0.73370.56521.5652-0.59210.29370.0911-0.03910.651-0.20320.5317-32.869963.383793.1076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 27:60)A27 - 60
2X-RAY DIFFRACTION2(chain A and resid 61:82)A61 - 82
3X-RAY DIFFRACTION3(chain A and resid 83:89)A83 - 89
4X-RAY DIFFRACTION4(chain A and resid 90:110)A90 - 110
5X-RAY DIFFRACTION5(chain A and resid 111:117)A111 - 117
6X-RAY DIFFRACTION6(chain A and resid 118:171)A118 - 171
7X-RAY DIFFRACTION7(chain A and resid 172:176)A172 - 176
8X-RAY DIFFRACTION8(chain A and resid 177:184)A177 - 184
9X-RAY DIFFRACTION9(chain A and resid 185:195)A185 - 195
10X-RAY DIFFRACTION10(chain A and resid 196:253)A196 - 253
11X-RAY DIFFRACTION11(chain A and resid 254:273)A254 - 273
12X-RAY DIFFRACTION12(chain A and resid 274:286)A274 - 286
13X-RAY DIFFRACTION13(chain A and resid 287:293)A287 - 293
14X-RAY DIFFRACTION14(chain A and resid 294:301)A294 - 301
15X-RAY DIFFRACTION15(chain A and resid 302:309)A302 - 309
16X-RAY DIFFRACTION16(chain A and resid 320:324)A320 - 324
17X-RAY DIFFRACTION17(chain A and resid 325:353)A325 - 353
18X-RAY DIFFRACTION18(chain A and resid 354:362)A354 - 362
19X-RAY DIFFRACTION19(chain A and resid 363:368)A363 - 368
20X-RAY DIFFRACTION20(chain A and resid 369:383)A369 - 383
21X-RAY DIFFRACTION21(chain B and resid 27:62)B27 - 62
22X-RAY DIFFRACTION22(chain B and resid 63:80)B63 - 80
23X-RAY DIFFRACTION23(chain B and resid 81:88)B81 - 88
24X-RAY DIFFRACTION24(chain B and resid 89:106)B89 - 106
25X-RAY DIFFRACTION25(chain B and resid 107:111)B107 - 111
26X-RAY DIFFRACTION26(chain B and resid 112:160)B112 - 160
27X-RAY DIFFRACTION27(chain B and resid 161:174)B161 - 174
28X-RAY DIFFRACTION28(chain B and resid 175:184)B175 - 184
29X-RAY DIFFRACTION29(chain B and resid 185:192)B185 - 192
30X-RAY DIFFRACTION30(chain B and resid 193:207)B193 - 207
31X-RAY DIFFRACTION31(chain B and resid 208:229)B208 - 229
32X-RAY DIFFRACTION32(chain B and resid 230:247)B230 - 247
33X-RAY DIFFRACTION33(chain B and resid 248:255)B248 - 255
34X-RAY DIFFRACTION34(chain B and resid 256:273)B256 - 273
35X-RAY DIFFRACTION35(chain B and resid 274:291)B274 - 291
36X-RAY DIFFRACTION36(chain B and resid 292:306)B292 - 306
37X-RAY DIFFRACTION37(chain B and resid 307:330)B307 - 330
38X-RAY DIFFRACTION38(chain B and resid 331:358)B331 - 358
39X-RAY DIFFRACTION39(chain B and resid 359:367)B359 - 367
40X-RAY DIFFRACTION40(chain B and resid 368:383)B368 - 383

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