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Yorodumi- PDB-3zsj: Crystal structure of Human Galectin-3 CRD in complex with Lactose... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zsj | |||||||||
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Title | Crystal structure of Human Galectin-3 CRD in complex with Lactose at 0.86 angstrom resolution | |||||||||
Components | GALECTIN-3 | |||||||||
Keywords | SUGAR 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 | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.86 Å | |||||||||
Authors | Saraboji, K. / Hakansson, M. / Diehl, C. / Nilsson, U.J. / Leffler, H. / Akke, M. / Logan, D.T. | |||||||||
Citation | Journal: Biochemistry / Year: 2012 Title: The Carbohydrate-Binding Site in Galectin-3 is Pre-Organized to Recognize a Sugar-Like Framework of Oxygens: Ultra-High Resolution Structures and Water Dynamics. Authors: Saraboji, K. / Hakansson, M. / Genheden, S. / Diehl, C. / Qvist, J. / Weininger, U. / Nilsson, U.J. / Leffler, H. / Ryde, U. / Akke, M. / Logan, D.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zsj.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zsj.ent.gz | 67 KB | Display | PDB format |
PDBx/mmJSON format | 3zsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/3zsj ftp://data.pdbj.org/pub/pdb/validation_reports/zs/3zsj | HTTPS FTP |
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-Related structure data
Related structure data | 3zskC 3zslC 3zsmC 2xg3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15701.049 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 113-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P17931 |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.2 % Description: STRUCTURE SOLVED BY STANDARD RIGID-BODY REFINEMENT USING REFMAC5 |
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Crystal grow | pH: 7.5 Details: 30% PEG 4000, 0.1M MGCL2, 0.008M BETA MERCAPTOETHANOL, 0.1M TRIS-HCL, PH 7.5, 0.4M NASCN |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.90778 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 13, 2009 |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.90778 Å / Relative weight: 1 |
Reflection | Resolution: 0.86→30 Å / Num. obs: 111079 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 6.13 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 0.86→0.88 Å / Redundancy: 4.03 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.8 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XG3 Resolution: 0.86→30 Å / Num. parameters: 13276 / Num. restraintsaints: 18944 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 39 / Occupancy sum hydrogen: 1115.6 / Occupancy sum non hydrogen: 1388.1 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.86→30 Å
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Refine LS restraints |
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