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- PDB-6kxb: Galectin-3 CRD binds to GalA trimer -

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Basic information

Entry
Database: PDB / ID: 6kxb
TitleGalectin-3 CRD binds to GalA trimer
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Galectin-3 CRD / GalA trimer
Function / homology
Function and homology information


negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / protein phosphatase inhibitor activity / negative regulation of T cell receptor signaling pathway / macrophage chemotaxis / positive chemotaxis / regulation of T cell proliferation / positive regulation of calcium ion import / chemoattractant activity / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / molecular condensate scaffold activity / neutrophil chemotaxis / secretory granule membrane / RNA splicing / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein-containing complex assembly / positive regulation of protein localization to plasma membrane / spliceosomal complex / mRNA processing / carbohydrate binding / protein phosphatase binding / collagen-containing extracellular matrix / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / 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: 1.5 Å
AuthorsSu, J.
CitationJournal: Glycobiology / Year: 2021
Title: Topsy-turvy binding of negatively charged homogalacturonan oligosaccharides to galectin-3.
Authors: Zheng, Y. / Su, J. / Miller, M.C. / Geng, J. / Xu, X. / Zhang, T. / Mayzel, M. / Zhou, Y. / Mayo, K.H. / Tai, G.
History
DepositionSep 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)16,2472
Polymers15,7011
Non-polymers5461
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint7 kcal/mol
Surface area7410 Å2
Unit cell
Length a, b, c (Å)35.880, 57.858, 61.562
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: 15701.049 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 alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-beta-D-galactopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpAa1-4DGalpAa1-4DGalpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112A-1b_1-5][a2112A-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GalpA]{[(4+1)][a-D-GalpA]{[(4+1)][a-D-GalpA]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging 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: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→19.34 Å / Num. obs: 21105 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.195

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R9A

4r9a


Resolution: 1.5→19.34 Å / SU ML: 0.15 / σ(F): 1.4 / Phase error: 19.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 2001 9.5 %
Rwork0.165 --
obs0.167 21053 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.99 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 37 201 1342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.21411360.16141342X-RAY DIFFRACTION100
1.54-1.580.25461460.16841336X-RAY DIFFRACTION100
1.58-1.630.21291400.1651342X-RAY DIFFRACTION100
1.63-1.680.23381370.16231329X-RAY DIFFRACTION99
1.68-1.740.24181430.16861348X-RAY DIFFRACTION100
1.74-1.810.22421330.16361365X-RAY DIFFRACTION100
1.81-1.890.20441510.15391340X-RAY DIFFRACTION100
1.89-1.990.19771420.14921343X-RAY DIFFRACTION100
1.99-2.110.1941480.16971357X-RAY DIFFRACTION100
2.11-2.280.24671410.17291347X-RAY DIFFRACTION99
2.28-2.50.2021430.17351361X-RAY DIFFRACTION99
2.51-2.870.2081440.1821376X-RAY DIFFRACTION99
2.87-3.610.18271450.14961403X-RAY DIFFRACTION99
3.61-19.340.1881520.15731463X-RAY DIFFRACTION99

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