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- PDB-6f6y: Crystal structure of galectin-3 CRD in complex with galactopentaose -

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Basic information

Entry
Database: PDB / ID: 6f6y
TitleCrystal structure of galectin-3 CRD in complex with galactopentaose
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / galectin / carbohydrate recognition
Function / homology
Function and homology information


negative regulation of protein tyrosine phosphatase activity / 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 / RUNX2 regulates genes involved in differentiation of myeloid cells / disaccharide binding / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration ...negative regulation of protein tyrosine phosphatase activity / 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 / RUNX2 regulates genes involved in differentiation of myeloid cells / disaccharide binding / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration / 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 / positive chemotaxis / regulation of T cell proliferation / positive regulation of calcium ion import / macrophage chemotaxis / 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 / molecular condensate scaffold activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / 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 / 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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
4beta-beta-galactobiose / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.41 Å
AuthorsHakansson, M. / Andersen, M.C.F. / Clausen, M.H. / Logan, D.T.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Strategic ResearchGlycAct Denmark
CitationJournal: To Be Published
Title: Beta-(1-4)-d-galactans: synthesis and binding interactions with galectin-3
Authors: Andersen, M.C.F. / Boos, I. / Kinnaert, C. / Awan, S.I. / Pedersen, H.L. / Kracun, S.K. / Lanz, G. / Rydahl, M.G. / Kjaerulff, L. / Hakansson, M. / Kimbung, R. / Logan, D.T. / Gotfredsen, C. ...Authors: Andersen, M.C.F. / Boos, I. / Kinnaert, C. / Awan, S.I. / Pedersen, H.L. / Kracun, S.K. / Lanz, G. / Rydahl, M.G. / Kjaerulff, L. / Hakansson, M. / Kimbung, R. / Logan, D.T. / Gotfredsen, C.H. / Willats, W.G.T. / Clausen, M.H.
History
DepositionDec 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)16,0772
Polymers15,7351
Non-polymers3421
Water3,909217
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint5 kcal/mol
Surface area7160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.060, 58.200, 62.990
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: 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 (E. coli) / References: UniProt: P17931
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-galactopyranose / 4beta-beta-galactobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-galactobiose
DescriptorTypeProgram
DGalpb1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2112h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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 Matthews: 2.19 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 19 mg/ml Gal3C in 10 mM sodium phosphate buffer pH 7.5, 100 mM NaCl, 10 mM beta-mercaptoethanol, 0.02 % NaN3. 3.5 microlitres Gal3C were mixed with 3.5 microlitres 100 mM galactopentaose ...Details: 19 mg/ml Gal3C in 10 mM sodium phosphate buffer pH 7.5, 100 mM NaCl, 10 mM beta-mercaptoethanol, 0.02 % NaN3. 3.5 microlitres Gal3C were mixed with 3.5 microlitres 100 mM galactopentaose solution and incubated on ice for one hour. Crystals were obtained in 30% w/v PEG 4000, 0.1 M Tris/HCl pH 7.5, 0.1M MgCl2, 0.4M NaSCN, 8 mM beta-mercaptoethanol. Cryoprotectant contained an additional 11% glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2013 / Details: FOCUSING MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→27.7 Å / Num. obs: 25876 / % possible obs: 98.2 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.8
Reflection shellResolution: 1.41→1.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.351 / CC1/2: 0.885 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3ZSK

3zsk


Resolution: 1.41→27.699 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.28
RfactorNum. reflection% reflection
Rfree0.1533 1290 4.99 %
Rwork0.1164 --
obs0.1183 25842 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.41→27.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 23 217 1349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051299
X-RAY DIFFRACTIONf_angle_d1.241777
X-RAY DIFFRACTIONf_dihedral_angle_d12.976540
X-RAY DIFFRACTIONf_chiral_restr0.074199
X-RAY DIFFRACTIONf_plane_restr0.006234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.46650.21141240.1862371X-RAY DIFFRACTION88
1.4665-1.53320.15761420.13042750X-RAY DIFFRACTION100
1.5332-1.6140.14681430.10312723X-RAY DIFFRACTION100
1.614-1.71510.15761460.0982762X-RAY DIFFRACTION100
1.7151-1.84750.15671430.09592714X-RAY DIFFRACTION100
1.8475-2.03340.13261450.09332754X-RAY DIFFRACTION100
2.0334-2.32750.11771470.0972779X-RAY DIFFRACTION100
2.3275-2.93190.16291460.1172785X-RAY DIFFRACTION100
2.9319-27.70460.16431540.13392914X-RAY DIFFRACTION99

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