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- PDB-9gf1: Cysteine-less human Galectin-3 C173S mutant carbohydrate recognit... -

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Basic information

Entry
Database: PDB / ID: 9gf1
TitleCysteine-less human Galectin-3 C173S mutant carbohydrate recognition domain
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Galectin-3 / galectin / lectin / CRD
Function / homology
Function and homology information


negative regulation of NK T cell activation / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / mononuclear cell migration / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / signaling receptor inhibitor activity / negative regulation of T cell receptor signaling pathway / protein phosphatase inhibitor activity / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / regulation of T cell proliferation / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / neutrophil chemotaxis / epithelial cell differentiation / RNA splicing / secretory granule membrane / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / positive regulation of protein-containing complex assembly / molecular condensate scaffold activity / mRNA processing / : / carbohydrate binding / protein phosphatase binding / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
beta-lactose / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBlaha, J. / Dubanych, Y. / Skorepa, O. / Vanek, O.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science Foundation23-08490L Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLTC20078 Czech Republic
CitationJournal: To Be Published
Title: Galectin-3 carbohydrate recognition is solely responsible for its binding to the NK cell activation receptor NKp30.
Authors: Blaha, J. / Dubanych, Y. / Skorepa, O. / Vanek, O.
History
DepositionAug 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3576
Polymers15,8161
Non-polymers5415
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-23 kcal/mol
Surface area7290 Å2
Unit cell
Length a, b, c (Å)37.020, 58.047, 63.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Galectin-3 / Gal-3 / 35 kDa lectin / Carbohydrate-binding protein 35 / CBP 35 / Galactose-specific lectin 3 / ...Gal-3 / 35 kDa lectin / Carbohydrate-binding protein 35 / CBP 35 / Galactose-specific lectin 3 / Galactoside-binding protein / GALBP / IgE-binding protein / L-31 / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 15816.178 Da / Num. of mol.: 1 / Mutation: C173S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P17931
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 22% (w/v) sodium polyacrylamide 5100, 0.02M magnesium chloride, 0.1M HEPES pH 7.5

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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: 0.961107 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jun 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.961107 Å / Relative weight: 1
ReflectionResolution: 1.5→58.05 Å / Num. obs: 22417 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 10.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.045 / Rrim(I) all: 0.12 / Χ2: 0.98 / Net I/σ(I): 9.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.1 % / Num. unique obs: 1092 / CC1/2: 0.715 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDS20220820data reduction
Aimless0.7.13data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→42.746 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.413 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1859 1019 4.558 %
Rwork0.1606 21335 -
all0.162 --
obs-22354 99.546 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.507 Å2
Baniso -1Baniso -2Baniso -3
1-1.736 Å20 Å2-0 Å2
2---1.096 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 32 149 1289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131186
X-RAY DIFFRACTIONr_bond_other_d0.0030.0151140
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.6741614
X-RAY DIFFRACTIONr_angle_other_deg1.3921.6022626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6185143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4822265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.36515198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.349159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021337
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02281
X-RAY DIFFRACTIONr_nbd_refined0.1960.2145
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1520.21024
X-RAY DIFFRACTIONr_nbtor_refined0.1570.2535
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.2609
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.286
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.080.24
X-RAY DIFFRACTIONr_nbd_other0.1490.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.217
X-RAY DIFFRACTIONr_mcbond_it1.3681.517566
X-RAY DIFFRACTIONr_mcbond_other1.3631.515565
X-RAY DIFFRACTIONr_mcangle_it1.962.273711
X-RAY DIFFRACTIONr_mcangle_other1.9612.275712
X-RAY DIFFRACTIONr_scbond_it2.771.875620
X-RAY DIFFRACTIONr_scbond_other2.7691.876621
X-RAY DIFFRACTIONr_scangle_it4.1542.704903
X-RAY DIFFRACTIONr_scangle_other4.1512.706904
X-RAY DIFFRACTIONr_lrange_it5.78219.5041184
X-RAY DIFFRACTIONr_lrange_other5.21718.5681149
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.371910.29615290.316270.8080.83799.56980.281
1.539-1.5810.251900.25814840.25815790.8740.86899.68330.241
1.581-1.6270.247670.21914900.2215610.8710.90199.74380.202
1.627-1.6770.166610.19614360.19514990.9360.92299.86660.177
1.677-1.7320.212500.18213950.18314490.9260.94199.72390.168
1.732-1.7920.19690.17413400.17514150.9480.94499.5760.16
1.792-1.860.216670.18113100.18313810.9270.94799.71040.165
1.86-1.9360.214530.16312550.16513120.9480.95999.69510.151
1.936-2.0220.177580.1512000.15112610.9670.96699.76210.14
2.022-2.120.206680.15311360.15612150.9610.96899.09470.145
2.12-2.2340.187470.14911010.15111520.9620.9799.65280.142
2.234-2.370.134430.14410600.14311050.9790.97299.8190.137
2.37-2.5330.165470.1469920.14710440.9770.97599.52110.139
2.533-2.7350.142600.1478970.1479620.9720.97399.48020.143
2.735-2.9950.167370.1578610.1589030.9720.96999.44630.153
2.995-3.3460.144360.1387800.1388250.9770.97498.90910.138
3.346-3.860.185280.1336920.1357240.9670.97999.44750.133
3.86-4.7170.15220.136060.136310.9750.98599.52460.137
4.717-6.6310.277180.1794810.1825020.9730.97799.40240.187
6.631-42.7460.16570.2062900.2053090.9890.96496.11650.228

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