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

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Basic information

Entry
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 / homology
Function and homology information


negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / 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 / macrophage chemotaxis / regulation of T cell proliferation / 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 / molecular condensate scaffold activity / neutrophil chemotaxis / RNA splicing / secretory granule membrane / positive regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / mRNA processing / carbohydrate binding / collagen-containing extracellular matrix / protein phosphatase binding / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MULTIPLE ISOMORPHOUS METHOD / Resolution: 2.1 Å
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.
History
DepositionJan 22, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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)15,9872
Polymers15,6041
Non-polymers3831
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP212121

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Components

#1: Protein GALECTIN-3 /


Mass: 15603.933 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN (CRD)
Source method: isolated from a genetically manipulated source
Details: THE CRD WAS PRODUCED BY TYPE VII COLLAGENASE (SIGMA) DIGESTION OF THE N-TERMINAL DOMAIN
Source: (gene. exp.) Homo sapiens (human)
Description: THE CRD WAS PRODUCED BY TYPE VII COLLAGENASE (SIGMA) DIGESTION OF THE N-TERMINAL DOMAIN
Production host: Escherichia coli (E. coli) / References: UniProt: P17931
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % 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- ...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
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-15 mg/mlprotein1drop
21 mMlactose1dropcan be replaced by 30mM N-acetyllactosamine
327-35 %PEG40001reservoirto PEG6000
4100 mMTris-HCl1reservoirpH8.5
5100 mM1reservoirMgCl2
68 mM2-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 7955 / % possible obs: 99 % / Rmerge(I) obs: 0.052
Reflection
*PLUS
Num. measured all: 40093

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MULTIPLE ISOMORPHOUS METHOD / Resolution: 2.1→5 Å / σ(F): 2
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 ...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.
Rfactor% reflectionSelection details
Rfree0.24 10 %RANDOM
Rwork0.17 --
obs0.17 99 %-
Displacement parametersBiso mean: 20.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 26 120 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
LS refinement shellResolution: 2.1→3.13 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rwork0.206 204 -
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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