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Yorodumi- PDB-1a3k: X-RAY CRYSTAL STRUCTURE OF THE HUMAN GALECTIN-3 CARBOHYDRATE RECO... -
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-Basic information
Entry | Database: PDB / ID: 1a3k | |||||||||
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Title | X-RAY CRYSTAL STRUCTURE OF THE HUMAN GALECTIN-3 CARBOHYDRATE RECOGNITION DOMAIN (CRD) AT 2.1 ANGSTROM RESOLUTION | |||||||||
Components | GALECTIN-3 | |||||||||
Keywords | GALECTIN / GALAPTIN / LECTIN / IGE-BINDING PROTEIN | |||||||||
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 / epithelial cell differentiation / laminin binding / neutrophil chemotaxis / positive regulation of protein localization to plasma membrane / RNA splicing / secretory granule membrane / molecular condensate scaffold activity / negative regulation of extrinsic apoptotic signaling pathway / spliceosomal complex / positive regulation of protein-containing complex assembly / mRNA processing / protein phosphatase binding / carbohydrate 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MULTIPLE ISOMORPHOUS METHOD / Resolution: 2.1 Å | |||||||||
Authors | Seetharaman, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a3k.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a3k.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 1a3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a3k_validation.pdf.gz | 439.6 KB | Display | wwPDB validaton report |
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Full document | 1a3k_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 1a3k_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 1a3k_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a3k ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a3k | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: 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
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. obs: 7955 / % possible obs: 99 % / Rmerge(I) obs: 0.052 |
Reflection | *PLUS Num. measured all: 40093 |
-Processing
Software |
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Refinement | Method 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.
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Displacement parameters | Biso mean: 20.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→3.13 Å / Total num. of bins used: 25
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Xplor file |
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