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- PDB-5nf7: Structure of Galectin-3 CRD in complex with compound 1 -

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Basic information

Entry
Database: PDB / ID: 5nf7
TitleStructure of Galectin-3 CRD in complex with compound 1
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Galectin-3 CRD / cation-Pi interactions
Function / homology
Function and homology information


negative regulation of NK T cell activation / mononuclear cell migration / 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 / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / mononuclear cell migration / 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 / 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 / signaling receptor inhibitor activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / 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 / epithelial cell differentiation / neutrophil chemotaxis / 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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsRonin, C. / Atmanene, C. / Gautier, F.M. / Pilard, F.D. / Teletchea, S. / Ciesielski, F. / Hannah, V.V. / Grandjean, C.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Biophysical and structural characterization of mono/di-arylated lactosamine derivatives interaction with human galectin-3.
Authors: Atmanene, C. / Ronin, C. / Teletchea, S. / Gautier, F.M. / Djedaini-Pilard, F. / Ciesielski, F. / Vivat, V. / Grandjean, C.
History
DepositionMar 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3602
Polymers19,9351
Non-polymers4241
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.810, 58.160, 63.130
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 / 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: 19935.432 Da / Num. of mol.: 1
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)-N-acetyl-2-(acetylamino)-2-deoxy-beta-D-glucopyranosylamine


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5_1*NCC/3=O_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp1NAc2NAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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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 % sol: 27.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Tris HCl pH7.5; 30-34% PEG4000; 100mM MgCl2; 400mM NaSCN; 8mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 18898 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rsym value: 0.046 / Net I/σ(I): 26.4
Reflection shellResolution: 1.56→1.68 Å / Rsym value: 0.097

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZSL

3zsl


Resolution: 1.59→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.213 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18096 945 5 %RANDOM
Rwork0.14301 ---
obs0.1449 17953 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.365 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2---0.77 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 29 158 1295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191259
X-RAY DIFFRACTIONr_bond_other_d0.0010.021233
X-RAY DIFFRACTIONr_angle_refined_deg2.2641.9751730
X-RAY DIFFRACTIONr_angle_other_deg0.97532847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.015163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58423.8163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95915217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5631511
X-RAY DIFFRACTIONr_chiral_restr0.1540.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211441
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02308
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_it1.4081.219584
X-RAY DIFFRACTIONr_mcbond_other1.3711.216583
X-RAY DIFFRACTIONr_mcangle_it2.0731.828736
X-RAY DIFFRACTIONr_mcangle_other2.0831.831737
X-RAY DIFFRACTIONr_scbond_it2.791.556675
X-RAY DIFFRACTIONr_scbond_other2.7891.556675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1492.229983
X-RAY DIFFRACTIONr_long_range_B_refined5.89911.5051370
X-RAY DIFFRACTIONr_long_range_B_other5.68510.7491305
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.587→1.628 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 67 -
Rwork0.13 1279 -
obs--98.39 %

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