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Open data
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Basic information
Entry | Database: PDB / ID: 6qrn | ||||||
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Title | Galectin-10 complexed with ribose | ||||||
![]() | Galectin-10 | ||||||
![]() | IMMUNE SYSTEM / auto-crystallising / complex / carbohydrate-binding / Charcot-Leyden crystal | ||||||
Function / homology | ![]() regulation of activated T cell proliferation / regulation of T cell cytokine production / T cell apoptotic process / regulation of T cell anergy / cysteine-type endopeptidase activity involved in apoptotic process / carbohydrate binding / collagen-containing extracellular matrix / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Verstraete, K. / Verschueren, K.H.G. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.1 KB | Display | ![]() |
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PDB format | ![]() | 62.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.3 KB | Display | ![]() |
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Full document | ![]() | 443.2 KB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gkqC ![]() 6gksC ![]() 6gktC ![]() 6gkuC ![]() 6glwC ![]() 6glxC ![]() 5xrgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | 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.) ![]() ![]() ![]() |
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#2: Sugar | ChemComp-RIP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: PBS supplemented with 300 mM D-ribose. Cryoprotection: 25 % (w/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2015 |
Radiation | Monochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Displacement parameters | Biso mean: 14.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.4→43.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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