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- PDB-9fyj: N-terminal domain of human galectin-8 in complex with an alpha-ga... -

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Basic information

Entry
Database: PDB / ID: 9fyj
TitleN-terminal domain of human galectin-8 in complex with an alpha-galactoside ligand
ComponentsIsoform 1 of Galectin-8
KeywordsSUGAR BINDING PROTEIN / inhibitor / complex / drug design
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / plasma cell differentiation / T cell costimulation / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / extracellular space / membrane ...lymphatic endothelial cell migration / xenophagy / plasma cell differentiation / T cell costimulation / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / extracellular space / membrane / cytoplasm / cytosol
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsAdrover Forteza, J. / Puric, E. / Nilsson, U.J. / Anderluh, M. / Logan, D.T.
Funding supportEuropean Union, Sweden, Slovenia, 9items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765581European Union
European Union (EU)EUTOPIA PhD Co-tutelle grantEuropean Union
Swedish Research Council2020-03317 Sweden
Swedish Research Council2016-04855 Sweden
Slovenian Research AgencyP1-0208 Slovenia
Slovenian Research AgencyJ1-50026 Slovenia
European Cooperation in Science and Technology (COST) actionCA18103European Union
European Cooperation in Science and Technology (COST) actionCA18132European Union
European Regional Development FundOP20.05187 RI-SI-EATRISEuropean Union
CitationJournal: Commun Chem / Year: 2025
Title: Nanomolar inhibitor of the galectin-8 N-terminal domain binds via a non-canonical cation-pi interaction.
Authors: Puric, E. / Hassan, M. / Sjovall, F. / Tomasic, T. / Pevec, M. / Lah, J. / Forteza, J.A. / Sundin, A. / Leffler, H. / Nilsson, U.J. / Logan, D.T. / Anderluh, M.
History
DepositionJul 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 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: Isoform 1 of Galectin-8
B: Isoform 1 of Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7345
Polymers34,5642
Non-polymers1,1703
Water6,810378
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-15 kcal/mol
Surface area14890 Å2
Unit cell
Length a, b, c (Å)53.689, 62.280, 84.791
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Isoform 1 of Galectin-8 / Gal-8 / Po66 carbohydrate-binding protein / Po66-CBP / Prostate carcinoma tumor antigen 1 / PCTA-1


Mass: 17281.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214
#2: Chemical ChemComp-A1IHE / 2-[[(2~{R},3~{R},4~{S},5~{S},6~{R})-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxymethyl)-5-oxidanyl-3-prop-2-ynoxy-oxan-4-yl]oxymethyl]-3-methyl-benzimidazole-5-carboxylic acid


Mass: 567.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H24Cl2N2O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.05 Å3/Da / Density % sol: 39.94 % / Description: flat plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Drops consisted of 2 ul galectin-8N at 13.1 mg/ml in PBS buffer, 1 mM ligand, 5% DMSO mixed with 2 ul of reservoir solution consisting of 35% (w/v) Morpheus precipitant mix 4, 0.16 M ...Details: Drops consisted of 2 ul galectin-8N at 13.1 mg/ml in PBS buffer, 1 mM ligand, 5% DMSO mixed with 2 ul of reservoir solution consisting of 35% (w/v) Morpheus precipitant mix 4, 0.16 M Morpheus alcohol mix, 61 mM MES, 39 mM imidazole, pH 7.5. Morpheus precipitant mix 4 is made up of 25% (w/v) each of methane pentane diol (MPD), polyethylene glycol (PEG) 1000 and PEG 3350. Morpheus alcohol mix contains 0.2 M each of 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol and 1,3-propanediol (1.2 M total).
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.08→45.4 Å / Num. obs: 119679 / % possible obs: 98 % / Redundancy: 12.4 % / Biso Wilson estimate: 14.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.015 / Rrim(I) all: 0.056 / Net I/σ(I): 18.4
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.465 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9860 / CC1/2: 0.559 / Rpim(I) all: 0.554 / Rrim(I) all: 1.573 / % possible all: 83.8

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5084refinement
Aimlessdata scaling
EDNAdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→42.4 Å / SU ML: 0.0972 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.0188
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1503 5966 4.99 %RANDOM
Rwork0.1324 113585 --
obs0.1333 119551 97.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.64 Å2
Refinement stepCycle: LAST / Resolution: 1.08→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 75 378 2830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812592
X-RAY DIFFRACTIONf_angle_d1.03433531
X-RAY DIFFRACTIONf_chiral_restr0.0935384
X-RAY DIFFRACTIONf_plane_restr0.0112474
X-RAY DIFFRACTIONf_dihedral_angle_d13.1981019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.090.30091600.29013017X-RAY DIFFRACTION78.48
1.09-1.110.26961620.2633176X-RAY DIFFRACTION83.33
1.11-1.120.25351840.24093285X-RAY DIFFRACTION85.93
1.12-1.130.23731590.22363490X-RAY DIFFRACTION90.79
1.13-1.150.22891800.20173724X-RAY DIFFRACTION96.66
1.15-1.160.19091810.18473804X-RAY DIFFRACTION99.01
1.16-1.180.19691940.16593857X-RAY DIFFRACTION99.8
1.18-1.20.19662220.15823810X-RAY DIFFRACTION99.88
1.2-1.220.18892100.14523826X-RAY DIFFRACTION100
1.22-1.240.17292170.14513783X-RAY DIFFRACTION99.93
1.24-1.260.16562170.14383837X-RAY DIFFRACTION100
1.26-1.280.17242030.13843870X-RAY DIFFRACTION99.98
1.28-1.310.16231960.13213843X-RAY DIFFRACTION100
1.31-1.330.16222230.12573812X-RAY DIFFRACTION100
1.33-1.360.15922150.12063819X-RAY DIFFRACTION100
1.36-1.390.13962150.11353865X-RAY DIFFRACTION100
1.39-1.430.13672050.10453822X-RAY DIFFRACTION100
1.43-1.470.13531840.10263873X-RAY DIFFRACTION100
1.47-1.510.14012010.10433867X-RAY DIFFRACTION100
1.51-1.560.13122100.10413866X-RAY DIFFRACTION100
1.56-1.610.12132100.10193869X-RAY DIFFRACTION100
1.61-1.680.13452140.10133863X-RAY DIFFRACTION100
1.68-1.750.13551990.10333885X-RAY DIFFRACTION100
1.75-1.850.11732190.10343870X-RAY DIFFRACTION99.98
1.85-1.960.13421990.1083903X-RAY DIFFRACTION100
1.96-2.110.13411790.11323923X-RAY DIFFRACTION100
2.11-2.330.13511980.11533927X-RAY DIFFRACTION100
2.33-2.660.14521970.13743961X-RAY DIFFRACTION100
2.66-3.350.15522040.14553997X-RAY DIFFRACTION100
3.36-42.40.15942090.15124141X-RAY DIFFRACTION99.61

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