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

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Basic information

Entry
Database: PDB / ID: 6glx
TitleStructure of galectin-10 in complex with the Fab fragment of a Charcot-Leyden crystal solubilizing antibody, 4E8
Components
  • Fab 4E8 - Heavy chain
  • Fab 4E8 - 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 / cysteine-type endopeptidase activity involved in apoptotic process / 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
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.396 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

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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 4E8 - Heavy chain
D: Fab 4E8 - Light chain
H: Fab 4E8 - Heavy chain
L: Fab 4E8 - Light chain


Theoretical massNumber of molelcules
Total (without water)136,0236
Polymers136,0236
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALLS shows that galectin-10 is a homodimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-53 kcal/mol
Surface area50550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.326, 150.449, 94.504
Angle α, β, γ (deg.)90.00, 96.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Galectin-10


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 His-tag (MASTTHHHHHHDTDIPTTGGGSRPDDDDKENLYFQ). Before crystallization experiments, the tag was removed by TEV protease.
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q05315
#2: Antibody Fab 4E8 - Heavy chain


Mass: 24747.504 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 4E8 - Light chain


Mass: 22635.832 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium nitrate 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980058 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980058 Å / Relative weight: 1
ReflectionResolution: 3.39→50 Å / Num. obs: 15646 / % possible obs: 98.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 81.873 Å2 / CC1/2: 0.987 / Rrim(I) all: 0.219 / Net I/σ(I): 5.09
Reflection shellResolution: 3.39→3.6 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 2489 / CC1/2: 0.365 / Rrim(I) all: 1.07 / % possible all: 98.1

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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: 3.396→46.965 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 42.34
RfactorNum. reflection% reflection
Rfree0.36 1050 6.72 %
Rwork0.303 --
obs0.3071 15616 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.396→46.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8685 0 0 0 8685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028917
X-RAY DIFFRACTIONf_angle_d0.6612161
X-RAY DIFFRACTIONf_dihedral_angle_d2.3955295
X-RAY DIFFRACTIONf_chiral_restr0.0451352
X-RAY DIFFRACTIONf_plane_restr0.0041556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3958-3.55030.39211260.35541796X-RAY DIFFRACTION98
3.5503-3.73740.43351120.34761868X-RAY DIFFRACTION100
3.7374-3.97140.41821300.34851817X-RAY DIFFRACTION99
3.9714-4.27790.39891380.31361833X-RAY DIFFRACTION99
4.2779-4.7080.38311310.29091819X-RAY DIFFRACTION99
4.708-5.38840.34041460.29011787X-RAY DIFFRACTION98
5.3884-6.78560.33571160.30781828X-RAY DIFFRACTION97
6.7856-46.96990.31671510.26821818X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -50.7527 Å / Origin y: -8.7701 Å / Origin z: 71.7569 Å
111213212223313233
T0.1346 Å2-0.0243 Å20.2126 Å2-0.4982 Å2-0.0427 Å2--0.1543 Å2
L0.6773 °20.2686 °20.1692 °2-0.9112 °2-0.4847 °2--0.9286 °2
S-0.1029 Å °-0.0443 Å °-0.0006 Å °0.0383 Å °0.2074 Å °-0.1813 Å °-0.0768 Å °-0.0722 Å °-0.0711 Å °
Refinement TLS groupSelection details: all

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