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- PDB-9kh4: Crystal structure of Galectin-8 N-CRD with N-acetyllactosamine -

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Basic information

Entry
Database: PDB / ID: 9kh4
TitleCrystal structure of Galectin-8 N-CRD with N-acetyllactosamine
ComponentsGalectin-8
KeywordsSUGAR BINDING PROTEIN / Crystal structure of Galectin-8 N-CRD with N-acetyllactosamine
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
NICKEL (II) ION / : / Galectin-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSu, J.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Arch.Biochem.Biophys. / Year: 2025
Title: Galectin-8 binding to alpha-1 antitrypsin is a physiological mechanism in healthy individuals but exacerbates the symptoms of alpha-1 antitrypsin deficiency.
Authors: Sayed, H. / Mayo, K.H. / Zhou, Y. / Tai, G. / Su, J.
History
DepositionNov 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4584
Polymers16,9931
Non-polymers4653
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.154, 49.154, 160.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

21A-599-

HOH

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Components

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


Mass: 16992.561 Da / Num. of mol.: 1
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-RNQ / ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2,4-bis(oxidanyl)oxan-3-yl]ethanamide


Mass: 383.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H25NO11 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.75→19.53 Å / Num. obs: 20585 / % possible obs: 98.6 % / Redundancy: 20 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 27.4
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.392 / Num. unique obs: 1138

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Processing

SoftwareName: PHENIX / Version: (1.21.1_5286: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→19.53 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 17.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2125 1985 9.75 %
Rwork0.1783 --
obs0.1816 20368 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 2 210 1426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041244
X-RAY DIFFRACTIONf_angle_d0.785
X-RAY DIFFRACTIONf_dihedral_angle_d13.503
X-RAY DIFFRACTIONf_chiral_restr0.061193
X-RAY DIFFRACTIONf_plane_restr0.006216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.25831380.22811284X-RAY DIFFRACTION100
1.79-1.840.22271430.21211313X-RAY DIFFRACTION100
1.84-1.90.23111430.20051319X-RAY DIFFRACTION100
1.9-1.960.27561290.24241231X-RAY DIFFRACTION94
1.96-2.030.22741430.18551306X-RAY DIFFRACTION100
2.03-2.110.28771400.24121295X-RAY DIFFRACTION98
2.11-2.20.20031410.16871312X-RAY DIFFRACTION100
2.2-2.320.2471420.19181323X-RAY DIFFRACTION99
2.32-2.470.17551440.1571338X-RAY DIFFRACTION100
2.47-2.660.20081440.16271322X-RAY DIFFRACTION100
2.66-2.920.18531460.17541357X-RAY DIFFRACTION100
2.92-3.340.20491470.17191354X-RAY DIFFRACTION100
3.34-4.20.21441240.15631141X-RAY DIFFRACTION82
4.21-19.530.18841610.16161488X-RAY DIFFRACTION100

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