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- PDB-6qrn: Galectin-10 complexed with ribose -

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Basic information

Entry
Database: PDB / ID: 6qrn
TitleGalectin-10 complexed with ribose
ComponentsGalectin-10
KeywordsIMMUNE SYSTEM / auto-crystallising / complex / carbohydrate-binding / Charcot-Leyden crystal
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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-ribopyranose / Galectin-10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVerstraete, K. / Verschueren, K.H.G.
Funding support Belgium, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2017-ADG Belgium
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
DepositionFeb 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8172
Polymers16,6671
Non-polymers1501
Water5,242291
1
A: Galectin-10
hetero molecules

A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6344
Polymers33,3342
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area2400 Å2
ΔGint3 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.139, 49.139, 261.025
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-678-

HOH

21A-685-

HOH

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Components

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


Mass: 16667.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MASTTHHHHHHDTDIPTTGGGSRPDDDDKENLYFQ (N-terminal sequence was cleaved off with TEV protease prior to crystallisation).
Source: (gene. exp.) Homo sapiens (human) / Gene: CLC, LGALS10, LGALS10A / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q05315
#2: Sugar ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PBS supplemented with 300 mM D-ribose. Cryoprotection: 25 % (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2015
RadiationMonochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 37263 / % possible obs: 97.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 18.9 % / Biso Wilson estimate: 10.71 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.107 / Net I/σ(I): 25.24
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 18.4 % / Mean I/σ(I) obs: 3.38 / Num. unique obs: 5725 / CC1/2: 0.901 / Rrim(I) all: 0.935 / % possible all: 95

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
TRUNCATEdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XRG

5xrg


Resolution: 1.4→43.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.064 / SU Rfree Cruickshank DPI: 0.056
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1867 5.01 %RANDOM
Rwork0.171 ---
obs0.172 37244 97.3 %-
Displacement parametersBiso mean: 14.63 Å2
Baniso -1Baniso -2Baniso -3
1--1.3531 Å20 Å20 Å2
2---1.3531 Å20 Å2
3---2.7062 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: 1 / Resolution: 1.4→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 0 10 291 1444
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011344HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.091831HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d493SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes33HARMONIC2
X-RAY DIFFRACTIONt_gen_planes198HARMONIC5
X-RAY DIFFRACTIONt_it1344HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.13
X-RAY DIFFRACTIONt_other_torsion15.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion169SEMIHARMONIC5
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_contact1920SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.452 138 5.03 %
Rwork0.448 2607 -
all0.448 2745 -
obs--95.05 %
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)
10.2705-0.06750.1230.3789-0.11870.5785-0.00740.01160.0036-0.03560.04550.0104-0.1697-0.0848-0.038-0.05230.00520.0003-0.02470.0051-0.0366-28.302622.412911.479
20.75781.15120.41392.14130.42311.21350.0674-0.0625-0.05620.0680.0150.00860.093-0.0738-0.0825-0.06820.0045-0.0085-0.03770.0015-0.0426-29.557810.70949.9329
30.44980.63050.10090.93510.10171.02260.05180.0018-0.0881-0.0128-0.0005-0.1620.010.0553-0.0513-0.06410.0053-0.0085-0.0458-0.0064-0.0157-18.683213.403111.7217
40.4511-0.0464-0.54761.59960.26251.21440.01090.02970.0178-0.08440.0345-0.0761-0.127-0.0401-0.0453-0.0492-0.00550.00820.0043-0.0012-0.0021-20.489622.70192.3222
50.62590.1070.05981.45570.21410.41310.02730.085-0.1652-0.13320.0583-0.18390.05030.0612-0.0855-0.0184-0.0050.0151-0.0144-0.0069-0.0134-21.960413.66090.1745
60.2980.77780.19292.74270.66661.2236-0.00960.0125-0.0765-0.01050.03270.18150.0517-0.1987-0.0231-0.1179-0.0043-0.0099-0.0475-0.0047-0.0447-30.787415.103512.117
70.4216-0.18731.06850.4321-0.19362.9585-0.0240.08290.0024-0.01230.03230.04430.030.0151-0.0083-0.04330.0024-0.00710.01040.01830.0133-31.640324.48051.9124
80.17860.02990.0361-0.0250.00230.0194-0.0080.02010.00730.00110.0031-0.0130.00420.0080.0049-0.01590.0068-0.0178-0.0101-0.00360.0262-19.85986.365614.3888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|4 - A|34 }
2X-RAY DIFFRACTION2{ A|35 - A|49 }
3X-RAY DIFFRACTION3{ A|50 - A|87 }
4X-RAY DIFFRACTION4{ A|88 - A|106 }
5X-RAY DIFFRACTION5{ A|107 - A|122 }
6X-RAY DIFFRACTION6{ A|123 - A|129 }
7X-RAY DIFFRACTION7{ A|130 - A|142 }
8X-RAY DIFFRACTION8{ A|500 - A|500 }

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