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- PDB-1a3k: X-RAY CRYSTAL STRUCTURE OF THE HUMAN GALECTIN-3 CARBOHYDRATE RECO... -

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Database: PDB / ID: 1a3k
TitleX-RAY CRYSTAL STRUCTURE OF THE HUMAN GALECTIN-3 CARBOHYDRATE RECOGNITION DOMAIN (CRD) AT 2.1 ANGSTROM RESOLUTION
ComponentsGALECTIN-3
KeywordsGALECTIN / GALAPTIN / LECTIN / IGE-BINDING PROTEIN
Function / homologyGalactoside-binding lectin / Galectin, carbohydrate recognition domain / RUNX2 regulates genes involved in differentiation of myeloid cells / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Advanced glycosylation endproduct receptor signaling / Neutrophil degranulation / Galactoside-binding lectin (galectin) domain profile. / Galectin-3 / Concanavalin A-like lectin/glucanase domain superfamily / negative regulation of immunological synapse formation ...Galactoside-binding lectin / Galectin, carbohydrate recognition domain / RUNX2 regulates genes involved in differentiation of myeloid cells / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Advanced glycosylation endproduct receptor signaling / Neutrophil degranulation / Galactoside-binding lectin (galectin) domain profile. / Galectin-3 / Concanavalin A-like lectin/glucanase domain superfamily / negative regulation of immunological synapse formation / negative regulation of protein tyrosine phosphatase activity / mononuclear cell migration / other organism cell / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of mononuclear cell migration / regulation of T cell apoptotic process / IgE binding / negative regulation of endocytosis / eosinophil chemotaxis / oligosaccharide binding / macrophage chemotaxis / protein phosphatase inhibitor activity / positive regulation of calcium ion import / regulation of myeloid cell differentiation / regulation of T cell proliferation / positive regulation of protein homodimerization activity / negative regulation of T cell receptor signaling pathway / positive chemotaxis / monocyte chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / immunological synapse / ficolin-1-rich granule membrane / laminin binding / chemoattractant activity / secretory granule membrane / spliceosomal complex / RNA splicing / epithelial cell differentiation / neutrophil chemotaxis / negative regulation of extrinsic apoptotic signaling pathway / mRNA processing / positive regulation of protein localization to plasma membrane / mitochondrial inner membrane / collagen-containing extracellular matrix / killing of cells of other organism / protein phosphatase binding / antimicrobial humoral immune response mediated by antimicrobial peptide / carbohydrate binding / innate immune response / neutrophil degranulation / cell surface / RNA binding / extracellular space / extracellular exosome / membrane / extracellular region / plasma membrane / nucleus / cytoplasm / Galectin-3
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / MULTIPLE ISOMORPHOUS METHOD / 2.1 Å resolution
AuthorsSeetharaman, J. / Kanigsberg, A. / Slaaby, R. / Leffler, H. / Barondes, S.H. / Rini, J.M.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: X-ray crystal structure of the human galectin-3 carbohydrate recognition domain at 2.1-A resolution.
Authors: Seetharaman, J. / Kanigsberg, A. / Slaaby, R. / Leffler, H. / Barondes, S.H. / Rini, J.M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Structure of S-Lectin, a Developmentally Regulated Vertebrate Beta-Galactoside-Binding Protein
Authors: Liao, D.I. / Kapadia, G. / Ahmed, H. / Vasta, G.R. / Herzberg, O.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: X-Ray Crystal Structure of the Human Dimeric S-Lac Lectin, L-14-II, in Complex with Lactose at 2.9-A Resolution
Authors: Lobsanov, Y.D. / Gitt, M.A. / Leffler, H. / Barondes, S.H. / Rini, J.M.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 22, 1998 / Release: Jul 15, 1998
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 15, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance
1.3Apr 4, 2018Structure modelData collectiondiffrn_source_diffrn_source.type

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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)16,0053
Polyers15,6041
Non-polymers4012
Water2,162120
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)37.600, 58.400, 64.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide GALECTIN-3 /


Mass: 15603.933 Da / Num. of mol.: 1
Details: THE CRD WAS PRODUCED BY TYPE VII COLLAGENASE (SIGMA) DIGESTION OF THE N-TERMINAL DOMAIN
Fragment: CARBOHYDRATE RECOGNITION DOMAIN (CRD) / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo
Description: THE CRD WAS PRODUCED BY TYPE VII COLLAGENASE (SIGMA) DIGESTION OF THE N-TERMINAL DOMAIN
Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P17931
#2: Chemical ChemComp-GAL / BETA-D-GALACTOSE


Mass: 180.156 Da / Num. of mol.: 1 / Formula: C6H12O6 / Galactose
#3: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6 / N-Acetylglucosamine
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 / Density percent sol: 48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: PROTEIN CRYSTALLIZED BY HANGING-DROP VAPOUR DIFFUSION METHOD FROM DROPS CONTAINING EQUAL VOLUMES OF PROTEIN(10-15MG/ML) IN CRYSTALLIZATION BUFFER CONTAINING 1MM LACTOSE OR 30 MM N-ACETYLLACTOSAMINE AND THE WELL SOLUTION COMPOSED OF 27-30% PEG 4000-6000, 100MM TRIS-HCL PH 8.5, 100 MM MGCL2, AND 8 MM 2-MERCAPTOETHANOL., vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
110-15 mg/mlproteindrop
21 mMlactosedropcan be replaced by 30mM N-acetyllactosamine
327-35 %PEG4000reservoirto PEG6000
4100 mMTris-HClreservoirpH8.5
5100 mMreservoirMgCl2
68 mM2-mercaptoethanolreservoir

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Data collection

DiffractionMean temperature: 287 kelvins
SourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Collection date: Dec 1, 1994
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.9 Å / D resolution low: 25 Å / Number obs: 7955 / Rmerge I obs: 0.052 / Percent possible obs: 99
Reflection
*PLUS
Number measured all: 40093

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefineMethod to determine structure: MULTIPLE ISOMORPHOUS METHOD
Details: THE STRUCTURE WAS SOLVED BY THE MULTIPLE ISOMORPHOUS REPLACEMENT METHOD. THE MODEL CONSISTS OF THE 137 AMINO ACID RESIDUE CARBOHYDRATE RECOGNITION DOMAIN IN COMPLEX WITH N-ACETYLLACTOSAMINE AND 120 WATER MOLECULES. THIS STRUCTURE REPRESENTS A CRD DETERMINED FROM A GALECTIN WHICH DOES NOT SHOW THE CANONICAL 2-FOLD SYMMETRIC DIMER ORGANIZATION SHOWN BY GALECTINS-1 AND -2. COMPARISON WITH GALECTINS-1 AND -2 PROVIDES AN EXPLANATION FOR THE DIFFERENCES IN CARBOHYDRATE-BINDING SPECIFICITY SHOWN BY GALECTIN-3, AND FOR THE FACT THAT IT FAILS TO FORM DIMERS BY ANALOGOUS CRD-CRD INTERACTIONS.
R Free selection details: RANDOM / Sigma F: 2
Displacement parametersB iso mean: 20.6 Å2
Least-squares processR factor R free: 0.24 / R factor R work: 0.17 / R factor obs: 0.17 / Highest resolution: 2.1 Å / Lowest resolution: 5 Å / Percent reflection R free: 1 / Percent reflection obs: 99
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 5 Å
Number of atoms included #LASTProtein: 1101 / Nucleic acid: 0 / Ligand: 26 / Solvent: 120 / Total: 1247
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS shellHighest resolution: 2.1 Å / R factor R work: 0.206 / Lowest resolution: 3.13 Å / Number reflection R work: 204 / Total number of bins used: 25 / Percent reflection obs: 77
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_3.1.PROTOPHCSDX_3.1.PRO
X-RAY DIFFRACTION2PARAM3_MOD_3.1.CHOTOPH3_3.1.CHO

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