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- PDB-5iuq: Galectin-3c in complex with Bisamido-thiogalactoside derivative 4 -

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Basic information

Entry
Database: PDB / ID: 5iuq
TitleGalectin-3c in complex with Bisamido-thiogalactoside derivative 4
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Gal3C / CRD
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
Chem-6E1 / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.121 Å
AuthorsNoresson, A.-L. / Aurelius, O. / Oberg, C.T. / Engstrom, O. / Sundin, A.P. / Hakansson, M. / Logan, D.T. / Leffler, H. / Nilsson, U.J.
Funding support Sweden, 5items
OrganizationGrant numberCountry
Swedish Research Council621-2009-5326 Sweden
Swedish Research Council621-2012-2978 Sweden
Olle Engkvist Byggmastare foundation Sweden
Royal Physiographic Society Sweden
European Community's Seventh Framework Program (FP7-2007-2013)HEALTH F2-2011-256986 project acronym PANACREAS
CitationJournal: To Be Published
Title: Controlling protein:ligand complex conformation through tuning of arginine-arene interactions: Synthetic and structural studies with 3-benzamido-2-sulfo-galactosides as galectin-3 ligands
Authors: Noresson, A.-L. / Aurelius, O. / Oberg, C.T. / Engstrom, O. / Sundin, A.P. / Hakansson, M. / Logan, D. / Leffler, H. / Nilsson, U.J.
History
DepositionMar 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4702
Polymers15,7011
Non-polymers7691
Water3,999222
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.064, 57.553, 62.202
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: 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: Chemical ChemComp-6E1 / 3-deoxy-3-[(2,3,5,6-tetrafluoro-4-methoxybenzene-1-carbonyl)amino]-beta-D-galactopyranosyl 3-deoxy-3-[(2,3,5,6-tetrafluoro-4-methoxybenzene-1-carbonyl)amino]-1-thio-beta-D-galactopyranoside


Mass: 768.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H28F8N2O12S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 9 mg/ml Gal3C with a reservoir of 100 mM Tris-HCl pH 7.8, 300 mM NaSCN, 100 mM MgCl2, 32% [w/v] PEG6000, 20 mM 2-Mercaptoethanol) cocrystallised with lactose (10 mM). Lactose displaced by soaking with ligand.

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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: Jun 30, 2013
Details: TOROIDAL MIRROR FOR HORIZONTAL AND VERTICAL FOCUSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→30 Å / Num. obs: 50259 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.76 % / Biso Wilson estimate: 10.97 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.35
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.12-1.20.5392.33198
1.2-1.40.2784.57199.7
1.4-1.60.11410.59199.8
1.6-1.70.06516.86199.8
1.7-1.80.1520.971100
1.8-20.08328.77199.9
2-2.50.0539.79199.9
2.5-30.03649.68199.8
3-40.02962.33199.9
4-60.02365.84199.4
6-100.02560.951100
100.01360.52191.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZSJ

3zsj


Resolution: 1.121→28.776 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.15
RfactorNum. reflection% reflection
Rfree0.1715 2579 5.13 %
Rwork0.1535 --
obs0.1544 50258 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 45.37 Å2 / Biso mean: 15.48 Å2 / Biso min: 6.51 Å2
Refinement stepCycle: final / Resolution: 1.121→28.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 51 222 1379
Biso mean--21.39 28.27 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0251318
X-RAY DIFFRACTIONf_angle_d2.2861825
X-RAY DIFFRACTIONf_chiral_restr0.129206
X-RAY DIFFRACTIONf_plane_restr0.014238
X-RAY DIFFRACTIONf_dihedral_angle_d15.317528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1211-1.14260.22111430.25792570271399
1.1426-1.16590.2851440.231326282772100
1.1659-1.19130.22021650.21442588275399
1.1913-1.2190.21381520.21522568272099
1.219-1.24950.21341450.19892618276399
1.2495-1.28330.18511310.19226562787100
1.2833-1.3210.21851330.181125922725100
1.321-1.36370.22351380.179326262764100
1.3637-1.41240.20761310.176626592790100
1.4124-1.4690.1761450.157826272772100
1.469-1.53580.1931440.154426362780100
1.5358-1.61680.1761370.142126622799100
1.6168-1.71810.14621530.138426412794100
1.7181-1.85070.16211660.136526272793100
1.8507-2.03690.15331500.122626672817100
2.0369-2.33150.1441380.127427032841100
2.3315-2.9370.1631300.147427432873100
2.937-28.7860.16021340.150928683002100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.53171.80920.49266.51231.22372.10250.03910.08540.107-0.10160.2369-0.3407-0.19570.3514-0.26520.0847-0.01770.04010.1535-0.05140.1816-0.20631.80481.8864
20.53580.1920.46043.23391.89752.24010.1023-0.032-0.02320.22560.05020.00840.18480.0841-0.14520.08390.00840.00480.0925-0.01250.0995-6.7755-7.73287.8165
30.80910.15850.50911.17991.28152.4172-0.02450.00430.1151-0.18660.0517-0.0501-0.31920.0132-0.02310.08590.00520.01130.0647-0.00190.0812-12.51254.0342.9173
40.8783-0.3501-0.58154.19412.43921.8650.05450.01880.1691-0.1303-0.09430.1567-0.3454-0.14650.04010.15090.04880.00450.1206-0.01360.1263-20.787611.23099.8138
53.4043-1.8607-0.46794.04192.36412.23490.01090.1540.0763-0.3286-0.17470.1031-0.5201-0.39230.04460.14030.0535-0.03970.153-0.00950.1004-21.6030.9738-5.7512
63.40150.81091.06430.34830.30871.41620.0223-0.17790.08130.0636-0.08120.1017-0.0519-0.18240.08360.12810.02590.00170.1326-0.02060.1372-17.33616.733814.2807
71.27011.11461.3493.20972.18273.07960.0498-0.0637-0.09730.1047-0.0156-0.00260.2298-0.1569-0.04280.0779-0.01390.00670.0775-0.00380.0645-13.2093-6.294912.4896
81.08720.33580.96591.07450.66141.29260.04950.0132-0.0670.0448-0.07110.06410.1209-0.21090.03820.0745-0.01580.00310.08090.00770.0726-17.2575-9.39232.6507
91.3646-0.23850.9123.47150.46031.92530.0686-0.0244-0.10140.15290.1177-0.04640.05970.1905-0.17930.06150.01280.02240.1136-0.02660.1054-3.9352-2.27257.1101
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 113 through 121 )A113 - 121
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 138 )A122 - 138
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 162 )A139 - 162
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 174 )A163 - 174
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 184 )A175 - 184
6X-RAY DIFFRACTION6chain 'A' and (resid 185 through 196 )A185 - 196
7X-RAY DIFFRACTION7chain 'A' and (resid 197 through 215 )A197 - 215
8X-RAY DIFFRACTION8chain 'A' and (resid 216 through 232 )A216 - 232
9X-RAY DIFFRACTION9chain 'A' and (resid 233 through 250 )A233 - 250

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