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- PDB-6glw: Structure of galectin-10 in complex with the Fab fragment of a Ch... -

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Basic information

Entry
Database: PDB / ID: 6glw
TitleStructure of galectin-10 in complex with the Fab fragment of a Charcot-Leyden crystal solubilizing antibody, 1D11
Components
  • Fab 1D11 - Heavy chain
  • Fab 1D11 - Light chain
  • Galectin-10
KeywordsSUGAR BINDING PROTEIN / Fab / galectin-10 / autocrystallizing / crystal solubilisation
Function / homology
Function and homology information


regulation of activated T cell proliferation / regulation of T cell cytokine production / T cell apoptotic process / regulation of T cell anergy / carbohydrate binding / collagen-containing extracellular matrix / cysteine-type endopeptidase activity / identical protein binding / cytosol
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Immunoglobulins ...Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Galectin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVerstraete, K. / Verschueren, K. / Savvides, S.N.
CitationJournal: Science / Year: 2019
Title: Protein crystallization promotes type 2 immunity and is reversible by antibody treatment.
Authors: Emma K Persson / Kenneth Verstraete / Ines Heyndrickx / Elien Gevaert / Helena Aegerter / Jean-Michel Percier / Kim Deswarte / Koen H G Verschueren / Ann Dansercoer / Delphine Gras / Pascal ...Authors: Emma K Persson / Kenneth Verstraete / Ines Heyndrickx / Elien Gevaert / Helena Aegerter / Jean-Michel Percier / Kim Deswarte / Koen H G Verschueren / Ann Dansercoer / Delphine Gras / Pascal Chanez / Claus Bachert / Amanda Gonçalves / Hanne Van Gorp / Hans De Haard / Christophe Blanchetot / Michael Saunders / Hamida Hammad / Savvas N Savvides / Bart N Lambrecht /
Abstract: Although spontaneous protein crystallization is a rare event in vivo, Charcot-Leyden crystals (CLCs) consisting of galectin-10 (Gal10) protein are frequently observed in eosinophilic diseases, such ...Although spontaneous protein crystallization is a rare event in vivo, Charcot-Leyden crystals (CLCs) consisting of galectin-10 (Gal10) protein are frequently observed in eosinophilic diseases, such as asthma. We found that CLCs derived from patients showed crystal packing and Gal10 structure identical to those of Gal10 crystals grown in vitro. When administered to the airways, crystalline Gal10 stimulated innate and adaptive immunity and acted as a type 2 adjuvant. By contrast, a soluble Gal10 mutein was inert. Antibodies directed against key epitopes of the CLC crystallization interface dissolved preexisting CLCs in patient-derived mucus within hours and reversed crystal-driven inflammation, goblet-cell metaplasia, immunoglobulin E (IgE) synthesis, and bronchial hyperreactivity (BHR) in a humanized mouse model of asthma. Thus, protein crystals may promote hallmark features of asthma and are targetable by crystal-dissolving antibodies.
History
DepositionMay 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-10
B: Galectin-10
C: Fab 1D11 - Heavy chain
D: Fab 1D11 - Light chain
H: Fab 1D11 - Heavy chain
L: Fab 1D11 - Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,3478
Polymers136,0936
Non-polymers2532
Water27,6531535
1
A: Galectin-10
B: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4513
Polymers41,2562
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint2 kcal/mol
Surface area12520 Å2
MethodPISA
2
C: Fab 1D11 - Heavy chain
D: Fab 1D11 - Light chain


Theoretical massNumber of molelcules
Total (without water)47,4192
Polymers47,4192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-24 kcal/mol
Surface area19370 Å2
MethodPISA
3
H: Fab 1D11 - Heavy chain
L: Fab 1D11 - Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4783
Polymers47,4192
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-25 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.634, 89.220, 249.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 3 types, 6 molecules ABCHDL

#1: Antibody Galectin-10 / Gal-10 / Charcot-Leyden crystal protein / CLC / Eosinophil lysophospholipase / Lysolecithin acylhydrolase


Mass: 20628.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Recombinant human galectin-10 was produced with an N-terminal cleavable purification tag (MASTTHHHHHHDTDIPTTGGGSRPDDDDKENLYFQ). Before crystallization experiments, the tag was removed by TEV protease.
Source: (gene. exp.) Homo sapiens (human) / Gene: CLC, LGALS10, LGALS10A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05315
#2: Antibody Fab 1D11 - Heavy chain


Mass: 24601.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): HEK293E / Production host: Homo sapiens (human)
#3: Antibody Fab 1D11 - Light chain


Mass: 22817.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): HEK293E / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 1537 molecules

#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1535 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate 0.1 M sodium acetate pH 4.0 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 107497 / % possible obs: 99.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 20.092 Å2 / CC1/2: 0.991 / Rrim(I) all: 0.234 / Net I/σ(I): 6.72
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 16333 / CC1/2: 0.444 / Rrim(I) all: 1.37 / % possible all: 94.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCL, 5X4G

1lcl

5x4g


Resolution: 1.9→27.82 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.127 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.211 5318 4.95 %RANDOM
Rwork0.167 ---
obs0.169 107466 98.4 %-
Displacement parametersBiso mean: 29.83 Å2
Baniso -1Baniso -2Baniso -3
1-2.2147 Å20 Å20 Å2
2---4.4775 Å20 Å2
3---2.2628 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.9→27.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8815 0 17 1555 10387
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019185HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.112521HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3053SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes198HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1354HARMONIC5
X-RAY DIFFRACTIONt_it9185HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.02
X-RAY DIFFRACTIONt_other_torsion15.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1192SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11117SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 312 5.01 %
Rwork0.23 5914 -
all0.232 6226 -
obs--78.34 %
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)
10.44360.1828-0.12550.3256-0.05531.16790.04430.01840.00920.11610.016-0.10390.19920.1207-0.0602-0.03950.03-0.00860.012-0.02680.0171-25.7709-5.2512-15.5077
21.26-0.4208-0.81122.05810.72921.91480.01080.03540.10270.01160.00390.00010.09020.0094-0.0147-0.06890.01670.0017-0.0072-0.01980.004-34.98530.5018-19.3625
30.130.15620.68340.50580.54810.00010.09120.1614-0.031-0.1468-0.0327-0.0409-0.03060.0817-0.0585-0.0430.04980.03540.06390.01310.01-28.30771.248-27.86
40.4876-0.76430.16171.01380.690.80310.03080.10340.18640.00310.0263-0.1837-0.04040.1652-0.0572-0.06260.01670.02080.0199-0.01280.0418-26.45675.6047-17.8361
50.17910.0668-0.05190-0.77391.67530.0697-0.18650.07580.1406-0.0499-0.06550.11720.2435-0.0198-0.03520.0365-0.01820.0199-0.0384-0.0035-24.8935-1.3814-8.3608
61.1565-0.02720.51811.01710.48741.86450.0418-0.00640.04430.25380.0513-0.13840.1565-0.0665-0.0931-0.06970.03260.0137-0.03930.0094-0.0675-37.0883-22.1382-25.0426
72.8453-1.8473-0.69422.15380.89771.24530.01530.02230.0374-0.02450.1027-0.0132-0.07710.0578-0.1181-0.03780.0458-0.00170.0071-0.02420.0061-29.3308-20.1585-32.9362
80.22480.1095-0.365100.39730.94360.02310.15460.1748-0.03460.0377-0.0179-0.1307-0.1393-0.0608-0.04030.06410.02110.01280.0120.0135-36.7762-14.1532-36.546
90.8193-0.5741-0.52591.07040.48620.6430.00970.1575-0.0910.029-0.00210.05470.0605-0.1203-0.0075-0.04920.0223-0.00330.0437-0.02530.0044-37.5262-25.0214-35.775
100.48311.24791.16691.2182-1.40760.8421-0.0032-0.0389-0.11590.00520.0116-0.00310.0912-0.1481-0.00840.00680.00560.0284-0.0027-0.0395-0.021-37.2324-29.1755-24.4343
113.7065-0.3898-0.38962.3601-1.30272.07490.09970.5347-0.1212-0.2256-0.0140.12260.37220.1444-0.0857-0.1060.0094-0.03190.0234-0.0966-0.0479-17.834-34.0215-63.0005
122.1154-0.9343-0.06321.7975-0.43522.45010.08770.4110.1719-0.1046-0.10580.0841-0.02440.06690.0181-0.10010.0145-0.00360.0731-0.0017-0.0404-19.0957-25.5133-60.5983
130.27080.2838-1.0600.11141.66290.05490.30820.14660.01230.06040.02460.0008-0.139-0.1153-0.12690.02710.01460.1192-0.0062-0.0261-11.7674-26.957-63.094
140.98472.137-0.99913.50372.22731.5355-0.0211-0.05440.03780.02730.1373-0.16830.01790.2251-0.1162-0.1173-0.00770.01470.1213-0.0212-0.075819.9313-23.237-83.9441
151.63440.51750.83282.14271.07982.94770.0012-0.0260.10350.02970.1162-0.1820.23250.2406-0.1174-0.08710.02080.01080.0501-0.0168-0.077216.2467-29.2694-81.9971
160.8943-1.6579-0.3910.2899-0.21652.9411-0.00250.0866-0.0444-0.04640.0341-0.06090.14510.2795-0.0316-0.05840.01110.00560.0804-0.026-0.041814.1634-29.3166-90.4035
173.8861-0.7389-0.09940-0.31210.73210.057-0.0060.23330.0358-0.0963-0.03860.0110.00640.0393-0.0994-0.006-0.0060.0027-0.0519-0.0099-0.5824-26.0201-46.998
180.71950.4433-0.44442.9631-2.32362.7921-0.00260.13720.105-0.1524-0.03960.0727-0.0490.30420.0422-0.0727-0.0257-0.0138-0.0053-0.0003-0.076417.9422-19.6337-72.5882
192.26571.18320.073.5353-1.12042.12690.06350.07760.3001-0.0141-0.09140.0658-0.13710.1480.0279-0.0191-0.03310.0220.0089-0.0133-0.027317.2532-15.0899-71.5377
203.5306-1.80542.5222.44330.440200.04190.04560.2594-0.03640.0561-0.1307-0.097-0.0537-0.0980.02390.02840.1004-0.1269-0.02920.0251-52.315136.9757-21.7382
211.4469-1.7266-1.30272.2061-0.94810.00030.0208-0.09280.14010.08090.2021-0.1759-0.28020.282-0.2230.0094-0.01590.00990.0096-0.07080.0513-43.538229.2994-15.4712
220.1341-0.5304-0.01041.4471-0.20311.72520.13990.04880.064-0.03690.0426-0.0933-0.2490.0422-0.1825-0.03680.0160.0478-0.04150.00010.0172-49.911526.5642-23.4752
230.5535-0.54641.16522.2383-0.292800.058-0.10330.058-0.1874-0.0161-0.0254-0.0634-0.1134-0.0419-0.02540.0323-0.0160.00410.0058-0.0506-70.973251.8501-11.4243
240.8682-0.17250.36271.03450.83366.97830.17680.0251-0.0055-0.165-0.0718-0.20250.03520.0819-0.1051-0.03860.05720.0001-0.05960.0124-0.0454-66.080747.9575-10.5068
252.21531.19452.24391.8512-1.87072.2243-0.05250.04950.13540.02390.06050.0153-0.28080.0413-0.00790.03210.0194-0.0075-0.0633-0.00440.0266-68.556158.964-4.7912
260.48090.61260.19670.7278-0.31410.0023-0.00420.15220.01790.00770.0294-0.0190.0694-0.1426-0.0252-0.03370.02540.00650.0402-0.00030.0146-65.514210.6705-19.5518
272.58151.78571.032901.17842.25330.0769-0.05920.1570.10350.062-0.0073-0.1983-0.2399-0.1389-0.02440.05050.06030.00760.02130.0082-61.625820.9384-12.1706
282.7533-0.148-1.99810-2.21930.98390.0433-0.2467-0.08110.0835-0.2114-0.2984-0.01330.1220.1681-0.0346-0.0276-0.03460.0371-0.02060.0102-57.942311.3765-6.6179
291.67350.0362-0.77660.28780.24521.0890.03820.0660.13340.07040.0395-0.03940.0901-0.1337-0.0777-0.04840.01970.0034-0.02810.0043-0.0104-64.935314.0661-15.7723
3000.7104-0.84070.67590.52170.226-0.07990.0717-0.05330.0861-0.0590.12920.0345-0.0550.1389-0.02910.05-0.0207-0.05410.01890.0446-81.697541.61-6.4791
311.2747-0.58170.40691.8253-1.72130.80470.0250.03910.20450.064-0.0318-0.0806-0.0180.02190.00680.02760.0519-0.0157-0.0609-0.01340.0219-76.36756.2358-14.7847
320-1.1052-0.68980.2655-0.82331.5637-0.06990.1103-0.0622-0.1304-0.0680.09250.093-0.04990.1380.00090.0122-0.0483-0.0582-0.0220.0283-85.412439.0499-12.38
330.6582-1.72420.29322.6971-0.88280.85780.00510.0022-0.1007-0.04850.00540.07690.0439-0.0855-0.01050.00650.0411-0.0404-0.0156-0.00620.0192-83.806547.9801-15.3644
344.227-2.91040.74080-1.84531.58690.0046-0.0401-0.20350.05520.00170.1130.113-0.1863-0.0063-0.00360.0524-0.028-0.02040.0024-0.0802-87.998850.4423-7.1072
351.03160.59530.25040.34830.61270.3944-0.0155-0.1085-0.07030.0002-0.015-0.0277-0.0016-0.05060.03050-0.05620.0413-0.0697-0.00140.0354-46.7995-13.9142-16.7105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|2 - A|34 }
2X-RAY DIFFRACTION2{ A|35 - A|57 }
3X-RAY DIFFRACTION3{ A|58 - A|87 }
4X-RAY DIFFRACTION4{ A|88 - A|129 }
5X-RAY DIFFRACTION5{ A|130 - A|140 }
6X-RAY DIFFRACTION6{ B|2 - B|34 }
7X-RAY DIFFRACTION7{ B|35 - B|57 }
8X-RAY DIFFRACTION8{ B|58 - B|87 }
9X-RAY DIFFRACTION9{ B|88 - B|129 }
10X-RAY DIFFRACTION10{ B|130 - B|139 }
11X-RAY DIFFRACTION11{ C|1 - C|33 }
12X-RAY DIFFRACTION12{ C|34 - C|83 }
13X-RAY DIFFRACTION13{ C|84 - C|129 }
14X-RAY DIFFRACTION14{ C|130 - C|153 }
15X-RAY DIFFRACTION15{ C|154 - C|204 }
16X-RAY DIFFRACTION16{ C|205 - C|224 }
17X-RAY DIFFRACTION17{ D|2 - D|110 }
18X-RAY DIFFRACTION18{ D|111 - D|154 }
19X-RAY DIFFRACTION19{ D|155 - D|214 }
20X-RAY DIFFRACTION20{ H|1 - H|17 }
21X-RAY DIFFRACTION21{ H|18 - H|33 }
22X-RAY DIFFRACTION22{ H|34 - H|121 }
23X-RAY DIFFRACTION23{ H|122 - H|153 }
24X-RAY DIFFRACTION24{ H|154 - H|213 }
25X-RAY DIFFRACTION25{ H|214 - H|230 }
26X-RAY DIFFRACTION26{ L|1 - L|35 }
27X-RAY DIFFRACTION27{ L|36 - L|50 }
28X-RAY DIFFRACTION28{ L|51 - L|63 }
29X-RAY DIFFRACTION29{ L|64 - L|110 }
30X-RAY DIFFRACTION30{ L|111 - L|125 }
31X-RAY DIFFRACTION31{ L|126 - L|141 }
32X-RAY DIFFRACTION32{ L|142 - L|154 }
33X-RAY DIFFRACTION33{ L|155 - L|201 }
34X-RAY DIFFRACTION34{ L|202 - L|216 }
35X-RAY DIFFRACTION35{ E|1 - E|2 }

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