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- PDB-6gks: X-ray structure determined from recombinant Charcot-Leyden crystal -

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Basic information

Entry
Database: PDB / ID: 6gks
TitleX-ray structure determined from recombinant Charcot-Leyden crystal
ComponentsGalectin-10
KeywordsSUGAR BINDING PROTEIN / recombinant / human / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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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)16,7592
Polymers16,6671
Non-polymers921
Water3,729207
1
A: Galectin-10
hetero molecules

A: Galectin-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5184
Polymers33,3342
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Unit cell
Length a, b, c (Å)48.900, 48.900, 258.629
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-373-

HOH

21A-399-

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: Recombinant human galectin-10 was produced with an N-terminal cleavable His-tag (MASTTHHHHHHDTDIPTTGGGSRPDDDDKENLYFQG). Upon TEV-mediated removal of the His-tag recombinant human galectin-10 ...Details: Recombinant human galectin-10 was produced with an N-terminal cleavable His-tag (MASTTHHHHHHDTDIPTTGGGSRPDDDDKENLYFQG). Upon TEV-mediated removal of the His-tag recombinant human galectin-10 autocrystallized in PBS buffer.
Source: (gene. exp.) Homo sapiens (human) / Gene: CLC, LGALS10, LGALS10A / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05315
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.4
Details: Upon removal of the N-terminal His-tag by TEV protease, at a protease:target protein ratio of 1:100 (w/w), recombinant galectin-10 autocrystallized in PBS buffer.
Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 39313 / % possible obs: 92.4 % / Redundancy: 17.9 % / Biso Wilson estimate: 10.1 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.076 / Net I/σ(I): 25.64
Reflection shellResolution: 1.34→1.42 Å / Redundancy: 14.6 % / Mean I/σ(I) obs: 5.8 / Num. unique obs: 4579 / Rrim(I) all: 0.72 / % possible all: 68.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LCL

1lcl


Resolution: 1.38→43.105 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.38
RfactorNum. reflection% reflection
Rfree0.1794 1833 4.88 %
Rwork0.1681 --
obs0.1686 37599 95.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.38→43.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 6 209 1352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051293
X-RAY DIFFRACTIONf_angle_d0.9091762
X-RAY DIFFRACTIONf_dihedral_angle_d7.386743
X-RAY DIFFRACTIONf_chiral_restr0.096186
X-RAY DIFFRACTIONf_plane_restr0.006232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.41730.21991060.19022345X-RAY DIFFRACTION84
1.4173-1.4590.18481230.18162668X-RAY DIFFRACTION95
1.459-1.50610.18041340.17012663X-RAY DIFFRACTION95
1.5061-1.560.16671500.1582652X-RAY DIFFRACTION95
1.56-1.62240.1851390.14962709X-RAY DIFFRACTION96
1.6224-1.69630.1571690.15612688X-RAY DIFFRACTION96
1.6963-1.78570.16861300.16062716X-RAY DIFFRACTION96
1.7857-1.89760.18351570.17122745X-RAY DIFFRACTION97
1.8976-2.04410.20111430.16622784X-RAY DIFFRACTION97
2.0441-2.24980.19071350.16252809X-RAY DIFFRACTION98
2.2498-2.57530.18481550.17532856X-RAY DIFFRACTION98
2.5753-3.24440.16821410.17492935X-RAY DIFFRACTION99
3.2444-43.12590.17621510.16693196X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -22.6572 Å / Origin y: 17.4215 Å / Origin z: 8.3791 Å
111213212223313233
T0.0523 Å20.0029 Å2-0.0033 Å2-0.0746 Å2-0.002 Å2--0.1163 Å2
L0.5492 °20.1074 °2-0.0926 °2-0.7766 °20.283 °2--1.9088 °2
S0.0358 Å °0.042 Å °-0.0076 Å °0.0125 Å °0.0043 Å °-0.0582 Å °-0.0716 Å °0.0105 Å °-0.0271 Å °
Refinement TLS groupSelection details: all

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