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

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Basic information

Entry
Database: PDB / ID: 6gku
TitleStructure of galectin-10 in complex with the Fab fragment of a Charcot-Leyden crystal solubilizing antibody, 6F5
Components
  • Fab 6F5 - Heavy Chain
  • Fab 6F5 - Light chain
  • Galectin-10
KeywordsSUGAR BINDING PROTEIN / Non-autocrystallizing / mutant / galectin-10
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 / 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
TRIETHYLENE GLYCOL / Galectin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 21, 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 23, 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
H: Fab 6F5 - Heavy Chain
L: Fab 6F5 - Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9545
Polymers67,7643
Non-polymers1902
Water14,826823
1
A: Galectin-10
H: Fab 6F5 - Heavy Chain
L: Fab 6F5 - Light chain
hetero molecules

A: Galectin-10
H: Fab 6F5 - Heavy Chain
L: Fab 6F5 - Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,90810
Polymers135,5276
Non-polymers3814
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)59.014, 146.186, 185.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-356-

HOH

21A-404-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 20685.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Recombinant human galectin-10 was produced with an N-terminal cleavable His-tag (MASTTHHHHHHDTDIPTTGGGSRPDDDDKENLYFQG). Before crystallization, the His-tag was cleaved by TEV protease.
Source: (gene. exp.) Homo sapiens (human) / Gene: CLC, LGALS10, LGALS10A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05315

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Antibody , 2 types, 2 molecules HL

#2: Antibody Fab 6F5 - Heavy Chain


Mass: 24206.004 Da / Num. of mol.: 1
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 6F5 - Light chain


Mass: 22872.350 Da / Num. of mol.: 1
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, 825 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 823 / 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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.04 M calcium chloride 0.04 M sodium formate 0.1 M PIPES pH 7.0 8% PEG Smear High

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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: 1.91→50 Å / Num. obs: 63019 / % possible obs: 99.7 % / Redundancy: 12.8 % / Biso Wilson estimate: 25.1 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.24 / Net I/σ(I): 7.67
Reflection shellResolution: 1.91→2.02 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 9927 / CC1/2: 0.4 / Rrim(I) all: 2.15 / % possible all: 98.3

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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: 1.91→47.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.113 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.129 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.111
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3144 5.02 %RANDOM
Rwork0.166 ---
obs0.168 62679 100 %-
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.4776 Å20 Å20 Å2
2--6.3098 Å20 Å2
3----2.8322 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.91→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4341 0 11 845 5197
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014585HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.096255HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1521SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes94HARMONIC2
X-RAY DIFFRACTIONt_gen_planes677HARMONIC5
X-RAY DIFFRACTIONt_it4585HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.89
X-RAY DIFFRACTIONt_other_torsion15.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion595SEMIHARMONIC5
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_contact5573SEMIHARMONIC4
LS refinement shellResolution: 1.91→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 224 4.9 %
Rwork0.218 4351 -
all0.22 4575 -
obs--99.83 %
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)
10.6079-0.26220.14991.135-0.00232.7759-0.0142-0.0371-0.09130.09630.09780.12230.26-0.1585-0.0836-0.0117-0.06670.054-0.0652-0.00580.013523.67152.916436.9129
22.71340.5916-0.85041.0371-0.51271.4903-0.03030.1215-0.0880.12470.0184-0.0580.04150.01550.01190.0314-0.03820.0454-0.0383-0.0185-0.002731.889810.20933.4747
31.48530.3452-0.66340.4208-0.98251.70050.0082-0.07410.13870.12630.02610.1073-0.1577-0.1379-0.03440.0338-0.02490.083-0.0369-0.01440.00724.482416.955737.4268
40.77560.1896-0.3150.62560.08592.2043-0.02980.11720.0901-0.080.10080.1896-0.0213-0.2273-0.071-0.0053-0.04940.0472-0.04760.00440.029622.768410.359228.8702
51.15790.21070.65141.882.91040.3627-0.01270.0083-0.1843-0.05230.00690.22440.0168-0.07090.00580.0032-0.0450.0331-0.0582-0.0044-0.003721.5953-0.256429.0879
61.64890.8921-0.91571.941-0.56930.89490.0731-0.4308-0.12060.017-0.1571-0.0810.16830.39190.084-0.01740.00320.00120.05040.0425-0.001656.323122.834317.6827
71.74850.7069-1.10210.531-0.23471.32380.0218-0.0615-0.1351-0.1023-0.0534-0.01030.15990.08390.0315-0.00140.0020.0239-0.04530.0148-0.017449.431922.254711.4453
80-0.14571.59700.83760-0.0277-0.06480.02680.04010.1158-0.12940.02510.2134-0.0881-0.0469-0.0310.0335-0.0293-0.033-0.020163.843435.98629.9431
93.5256-0.1807-0.56013.50841.11363.6983-0.1427-0.54420.20580.54420.2183-0.3555-0.042-0.0178-0.0755-0.0140.0399-0.051-0.017-0.0715-0.127763.749748.921225.4618
101.66380.52142.8610.0002-2.18344.0077-0.035-0.3015-0.02630.0306-0.011-0.13170.0990.08180.0460.08470.1178-0.1145-0.0235-0.0318-0.12970.507444.16826.4883
111.89420.93850.78441.2976-0.75092.49450.04610.11120.2556-0.24020.14340.40690.06280.0286-0.1895-0.0277-0.0272-0.0499-0.03550.0150.056832.694440.21969.3849
122.3669-0.9059-0.25372.5215-0.59121.6297-0.0206-0.0905-0.0686-0.0380.0680.36280.1672-0.147-0.0474-0.0376-0.02570.0121-0.05480.00010.000335.737630.101413.3958
131.4036-0.5533-0.53224.25240.81171.6905-0.0996-0.1065-0.04770.12090.11290.50930.104-0.0225-0.0132-0.0982-0.0166-0.0037-0.06990.0212-0.025332.954934.010915.3414
146.45621.11230.08124.08041.08341.18490.0005-0.1320.03170.04640.1482-0.517-0.05520.1968-0.1487-0.0738-0.05250.0065-0.0973-0.0589-0.059857.988759.56720.4968
154.98450.2629-0.5722.93641.1361.45910.00720.19690.257-0.21860.1457-0.5401-0.18160.1879-0.1529-0.0777-0.07250.025-0.0621-0.05180.005859.303759.590416.0832
160.0732.91040.03816.62971.36220.99570.00720.0280.1479-0.27390.1638-0.2897-0.2060.0079-0.1710.0185-0.08270.0305-0.0426-0.02210.038458.336968.521819.8887
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|141 }
6X-RAY DIFFRACTION6{ H|1 - H|33 }
7X-RAY DIFFRACTION7{ H|34 - H|111 }
8X-RAY DIFFRACTION8{ H|112 - H|127 }
9X-RAY DIFFRACTION9{ H|128 - H|201 }
10X-RAY DIFFRACTION10{ H|202 - H|222 }
11X-RAY DIFFRACTION11{ L|1 - L|23 }
12X-RAY DIFFRACTION12{ L|24 - L|50 }
13X-RAY DIFFRACTION13{ L|51 - L|110 }
14X-RAY DIFFRACTION14{ L|111 - L|154 }
15X-RAY DIFFRACTION15{ L|155 - L|191 }
16X-RAY DIFFRACTION16{ L|192 - L|214 }

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