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- PDB-7be3: Human Galectin-3 in complex with LacdiNAc -

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Basic information

Entry
Database: PDB / ID: 7be3
TitleHuman Galectin-3 in complex with LacdiNAc
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Galectin-3 / LacdiNAc / LDN / glycan / lectin / immune
Function / homology
Function and homology information


: / 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 / mononuclear cell migration / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding ...: / 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 / mononuclear cell migration / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding / 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 / regulation of T cell proliferation / positive chemotaxis / macrophage chemotaxis / 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 / neutrophil chemotaxis / RNA splicing / secretory granule membrane / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / spliceosomal complex / positive regulation of protein-containing complex assembly / mRNA processing / carbohydrate binding / protein phosphatase binding / collagen-containing extracellular matrix / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / RNA binding / extracellular space / 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: 1.25 Å
AuthorsTrovao, F. / Carvalho, A.L.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT) Portugal
CitationJournal: Chemistry / Year: 2021
Title: Structural Insights into the Molecular Recognition Mechanism of the Cancer and Pathogenic Epitope, LacdiNAc by Immune-Related Lectins.
Authors: Lima, C.D.L. / Coelho, H. / Gimeno, A. / Trovao, F. / Diniz, A. / Dias, J.S. / Jimenez-Barbero, J. / Corzana, F. / Carvalho, A.L. / Cabrita, E.J. / Marcelo, F.
History
DepositionDec 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2874
Polymers15,7351
Non-polymers5523
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-2 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.039, 58.048, 62.286
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 15735.129 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 BL21(DE3) (bacteria) / References: UniProt: P17931
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpNAcb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-GalpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 32% PEG 4000, 100 mM Tris-HCl pH 7.5, 100 mM Magnesium chloride, 8 mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.25→31.19 Å / Num. all: 287616 / Num. obs: 36869 / % possible obs: 99.85 % / Redundancy: 7.8 % / Biso Wilson estimate: 14.34 Å2 / CC1/2: 1 / Net I/σ(I): 20.71
Reflection shellResolution: 1.25→1.295 Å / Num. measured obs: 27673 / Num. unique obs: 3611 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zsl

3zsl


Resolution: 1.25→31.19 Å / SU ML: 0.159 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 20.3602
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1949 3480 4.99 %
Rwork0.1704 66273 -
obs0.1717 36843 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.06 Å2
Refinement stepCycle: LAST / Resolution: 1.25→31.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 36 184 1329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451214
X-RAY DIFFRACTIONf_angle_d0.84171653
X-RAY DIFFRACTIONf_chiral_restr0.0929187
X-RAY DIFFRACTIONf_plane_restr0.006216
X-RAY DIFFRACTIONf_dihedral_angle_d24.9849166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.32911670.36332643X-RAY DIFFRACTION99.47
1.27-1.290.27311260.34272684X-RAY DIFFRACTION99.89
1.29-1.30.38441460.32182579X-RAY DIFFRACTION99.67
1.3-1.320.31451110.31122699X-RAY DIFFRACTION99.89
1.32-1.350.3021490.29022620X-RAY DIFFRACTION99.64
1.35-1.370.30441300.28352612X-RAY DIFFRACTION99.67
1.37-1.390.2491450.25962716X-RAY DIFFRACTION99.79
1.39-1.420.27431260.22442672X-RAY DIFFRACTION99.89
1.42-1.450.22281600.21512609X-RAY DIFFRACTION99.75
1.45-1.480.20821330.18752651X-RAY DIFFRACTION99.93
1.48-1.520.21580.18442643X-RAY DIFFRACTION99.93
1.52-1.550.23341580.1832613X-RAY DIFFRACTION99.78
1.55-1.60.17941140.16812691X-RAY DIFFRACTION100
1.6-1.640.1771190.15532685X-RAY DIFFRACTION99.96
1.64-1.70.15211330.1512629X-RAY DIFFRACTION100
1.7-1.760.19541040.15312704X-RAY DIFFRACTION100
1.76-1.830.20621360.15292654X-RAY DIFFRACTION100
1.83-1.910.20431370.1572640X-RAY DIFFRACTION99.96
1.91-2.010.14771290.14292711X-RAY DIFFRACTION100
2.01-2.140.15711450.16032614X-RAY DIFFRACTION99.96
2.14-2.30.18981440.15512645X-RAY DIFFRACTION99.93
2.3-2.530.19771480.16292660X-RAY DIFFRACTION99.96
2.53-2.90.1771500.17022638X-RAY DIFFRACTION99.93
2.9-3.650.19171400.14832646X-RAY DIFFRACTION99.93
3.65-31.190.18051720.1522615X-RAY DIFFRACTION99.46
Refinement TLS params.Method: refined / Origin x: -13.0710315217 Å / Origin y: -0.442037319623 Å / Origin z: 6.0469279358 Å
111213212223313233
T0.102867986931 Å2-0.00378149785688 Å20.0113997607591 Å2-0.116035051729 Å2-0.00901477127024 Å2--0.114482892072 Å2
L0.335021914232 °20.0305726032977 °20.126985630357 °2-0.908349037286 °20.572078581595 °2--0.911688172798 °2
S0.00310851559237 Å °-0.00108012030283 Å °0.037020620554 Å °-0.0184041748263 Å °0.00881413747384 Å °-0.00453216218243 Å °-0.0251138787284 Å °-0.0233404176946 Å °0.00189020369365 Å °
Refinement TLS groupSelection details: all

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