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- PDB-6g0v: Human Galectin-3 in complex with a TF tumor-associated antigen mimetic -

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Basic information

Entry
Database: PDB / ID: 6g0v
TitleHuman Galectin-3 in complex with a TF tumor-associated antigen mimetic
ComponentsGalectin-3
KeywordsCELL ADHESION / Galectin-3 / Thomsen-Friedenreich / tumour antigen / cancer / TF-mimetic
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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-EGZ / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.09 Å
AuthorsTrovao, F.G. / Santarsia, S. / Carvalho, A.L.
Funding support Portugal, 2items
OrganizationGrant numberCountry
FEDERPOCI-01-0145-FEDER-007728 Portugal
FCT/MCTESUID/Multi/04378/2013 Portugal
CitationJournal: ChemMedChem / Year: 2018
Title: Molecular Recognition of a Thomsen-Friedenreich Antigen Mimetic Targeting Human Galectin-3.
Authors: Santarsia, S. / Grosso, A.S. / Trovao, F. / Jimenez-Barbero, J. / Carvalho, A.L. / Nativi, C. / Marcelo, F.
History
DepositionMar 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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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)16,2663
Polymers15,7351
Non-polymers5312
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.900, 58.200, 62.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: Chemical ChemComp-EGZ / (3~{R},5~{R},6~{S},7~{S},8~{R},13~{S})-5-(hydroxymethyl)-7-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-oxidanyl-11-oxidanylidene-2,4-dioxa-9-thia-12-azatricyclo[8.4.0.0^{3,8}]tetradec-1(10)-ene-13-carboxylic acid


Mass: 495.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H25NO13S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 34% (w/v) PEG 400, 100 mM Tris-HCl (pH 7.5), 100 mM MgCl2, 8 mM B-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.09→42.675 Å / Num. obs: 41602 / % possible obs: 76.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 11.85 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.019 / Net I/σ(I): 17.8
Reflection shellResolution: 1.09→1.14 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.09→42.675 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 20.49
RfactorNum. reflection% reflection
Rfree0.1771 2057 4.95 %
Rwork0.1528 --
obs0.1541 41557 76.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.63 Å2 / Biso mean: 18.3903 Å2 / Biso min: 8.65 Å2
Refinement stepCycle: final / Resolution: 1.09→42.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 58 223 1390
Biso mean--31.79 29.05 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071265
X-RAY DIFFRACTIONf_angle_d1.0351737
X-RAY DIFFRACTIONf_chiral_restr0.088196
X-RAY DIFFRACTIONf_plane_restr0.007229
X-RAY DIFFRACTIONf_dihedral_angle_d14.865497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0974-1.12290.2486440.244394899228
1.1229-1.1510.2698560.22271251130737
1.151-1.18210.228840.21321651173548
1.1821-1.21690.1848950.19222259235466
1.2169-1.25620.22711750.18852916309188
1.2562-1.30110.18411200.17782470259093
1.3011-1.35320.19221880.18193177336594
1.3532-1.41480.21011560.17753245340194
1.4148-1.48930.20611520.16612757290980
1.4893-1.58270.17661540.15572819297383
1.5827-1.70490.16661630.15433330349396
1.7049-1.87640.15831410.15093044318589
1.8764-2.14790.17251630.1372981314495
2.1479-2.70610.15811890.1483214340392
2.7061-42.7070.17841770.14213438361593
Refinement TLS params.Method: refined / Origin x: -13.0988 Å / Origin y: -0.0968 Å / Origin z: 6.1645 Å
111213212223313233
T0.0761 Å2-0.0029 Å20.0162 Å2-0.0687 Å2-0.0041 Å2--0.0854 Å2
L0.3728 °20.0261 °20.2356 °2-1.3287 °20.8499 °2--1.6125 °2
S-0.0006 Å °-0.0194 Å °0.0487 Å °-0.0058 Å °0.0028 Å °0.0023 Å °-0.049 Å °-0.0178 Å °-0.0028 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA113 - 250
2X-RAY DIFFRACTION1allB1 - 74
3X-RAY DIFFRACTION1allB75 - 153
4X-RAY DIFFRACTION1allB154 - 157
5X-RAY DIFFRACTION1allB158 - 223
6X-RAY DIFFRACTION1allB224 - 227
7X-RAY DIFFRACTION1allC1
8X-RAY DIFFRACTION1allD1

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