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- PDB-9nqo: Crystal structure of Galectin-3 in complex with FN3 -

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Basic information

Entry
Database: PDB / ID: 9nqo
TitleCrystal structure of Galectin-3 in complex with FN3
ComponentsGalectin-3,Galectin-3,Galectin-3 in complex FN3
KeywordsPROTEIN BINDING / Monobody / Fn3-con / S100A7-psoriasin / protein binding complex
Function / homology
Function and homology information


negative regulation of NK T cell activation / mononuclear cell migration / negative regulation of immunological synapse formation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / disaccharide binding / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / receptor ligand inhibitor activity / negative regulation of endocytosis / positive regulation of mononuclear cell migration ...negative regulation of NK T cell activation / mononuclear cell migration / negative regulation of immunological synapse formation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / disaccharide binding / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / receptor ligand inhibitor activity / negative regulation of endocytosis / positive regulation of mononuclear cell migration / IgE binding / eosinophil chemotaxis / macrophage chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / regulation of T cell proliferation / protein phosphatase inhibitor activity / positive chemotaxis / chemoattractant activity / positive regulation of calcium ion import / monocyte chemotaxis / immunological synapse / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / negative regulation of T cell receptor signaling pathway / neutrophil chemotaxis / spliceosomal complex / epithelial cell differentiation / laminin binding / RNA splicing / secretory granule membrane / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / positive regulation of protein-containing complex assembly / mRNA processing / carbohydrate binding / protein phosphatase binding / extracellular matrix / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / : / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsGuo, Z. / Alexandrov, K. / Mutschler, R. / Caputo, A. / Cui, Z.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: The crystal structure of Galectin-3 in complex with FN3
Authors: Guo, Z. / Alexandrov, K. / Mutschler, R. / Cui, Z. / Caputo, A.
History
DepositionMar 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-3,Galectin-3,Galectin-3 in complex FN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8992
Polymers29,8031
Non-polymers961
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.614, 50.234, 97.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Galectin-3,Galectin-3,Galectin-3 in complex FN3 / 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: 29803.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2
Production host: bacterial enrichment culture S2-E1 (others)
References: UniProt: P17931
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.32 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.5M ammonium sulfate with 0.1M BIS-TRIS pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Aug 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.04→44.67 Å / Num. obs: 39872 / % possible obs: 99.9 % / Redundancy: 8.4 % / CC1/2: 1 / Net I/σ(I): 4.6
Reflection shellResolution: 2.04→2.1 Å / Num. unique obs: 5995 / CC1/2: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→44.67 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.197 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.4 693 5 %RANDOM
Rwork0.3 ---
obs0.3 13150 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.561 Å2
Baniso -1Baniso -2Baniso -3
1-39.13 Å20 Å20 Å2
2---22.98 Å2-0 Å2
3----16.15 Å2
Refinement stepCycle: 1 / Resolution: 2.04→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 5 60 1822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121817
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.811.8112482
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3965228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.84559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44710290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1270.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021384
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6093.824906
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.886.8411130
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.444.008911
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.96450.542754
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.043→2.096 Å
RfactorNum. reflection% reflection
Rfree0.849 63 -
Rwork0.8 913 -
obs--97.8 %

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