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Yorodumi- PDB-2eal: Crystal structure of human galectin-9 N-terminal CRD in complex w... -
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-Basic information
Entry | Database: PDB / ID: 2eal | |||||||||
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Title | Crystal structure of human galectin-9 N-terminal CRD in complex with Forssman pentasaccharide | |||||||||
Components | Galectin-9 | |||||||||
Keywords | SUGAR BINDING PROTEIN / beta sandwich / carbohydrate binding protein / galectin | |||||||||
Function / homology | Function and homology information positive regulation of activated T cell autonomous cell death / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / Interleukin-2 family signaling / positive regulation of dendritic cell apoptotic process / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / natural killer cell tolerance induction / negative regulation of mast cell degranulation / positive regulation of dendritic cell chemotaxis / positive regulation of dendritic cell differentiation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway ...positive regulation of activated T cell autonomous cell death / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / Interleukin-2 family signaling / positive regulation of dendritic cell apoptotic process / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / natural killer cell tolerance induction / negative regulation of mast cell degranulation / positive regulation of dendritic cell chemotaxis / positive regulation of dendritic cell differentiation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of transforming growth factor beta production / galactose binding / negative regulation of natural killer cell mediated cytotoxicity / disaccharide binding / galactoside binding / positive regulation of interleukin-13 production / negative regulation of chemokine production / positive regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of monocyte chemotactic protein-1 production / positive regulation of interleukin-4 production / p38MAPK cascade / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / maternal process involved in female pregnancy / positive regulation of interleukin-12 production / ERK1 and ERK2 cascade / response to interleukin-1 / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / female pregnancy / cellular response to virus / cellular response to type II interferon / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / chemotaxis / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / positive regulation of NF-kappaB transcription factor activity / carbohydrate binding / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / response to lipopolysaccharide / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / inflammatory response / negative regulation of gene expression / positive regulation of gene expression / enzyme binding / extracellular space / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Nagae, M. / Nakamura-Tsuruta, S. / Nishi, N. / Nakamura, T. / Hirabayashi, J. / Wakatsuki, S. / Kato, R. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural analysis of the human galectin-9 N-terminal carbohydrate recognition domain reveals unexpected properties that differ from the mouse orthologue. Authors: Nagae, M. / Nishi, N. / Nakamura-Tsuruta, S. / Hirabayashi, J. / Wakatsuki, S. / Kato, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eal.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eal.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 2eal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2eal_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2eal_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2eal_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 2eal_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/2eal ftp://data.pdbj.org/pub/pdb/validation_reports/ea/2eal | HTTPS FTP |
-Related structure data
Related structure data | 2eakC 2eag 2eah 2eai 2eaj 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16358.354 Da / Num. of mol.: 2 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00182 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% w/v Polyethylene Glycol 4000, 0.1M Sodium Acetate trihydrate pH 4.6, 0.2M Ammonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→57.74 Å / Num. all: 24511 / Num. obs: 23876 / % possible obs: 99.1 % / Redundancy: 5.1 % / Rsym value: 0.099 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 4.8 % / Num. unique all: 2384 / Rsym value: 0.352 / % possible all: 97.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→57.74 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.284 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.842 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→57.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.852→1.9 Å / Total num. of bins used: 20
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