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Yorodumi- PDB-2yy1: Crystal structure of N-terminal domain of human galectin-9 contai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yy1 | |||||||||
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Title | Crystal structure of N-terminal domain of human galectin-9 containing L-acetyllactosamine | |||||||||
Components | Galectin-9 | |||||||||
Keywords | SUGAR BINDING PROTEIN / suger binding / galectin / human / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information positive regulation of activated T cell autonomous cell death / Interleukin-2 family signaling / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / positive regulation of dendritic cell apoptotic process / disaccharide binding / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of mast cell degranulation / positive regulation of dendritic cell chemotaxis / positive regulation of dendritic cell differentiation / galactoside binding ...positive regulation of activated T cell autonomous cell death / Interleukin-2 family signaling / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / positive regulation of dendritic cell apoptotic process / disaccharide binding / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of mast cell degranulation / positive regulation of dendritic cell chemotaxis / positive regulation of dendritic cell differentiation / galactoside binding / 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 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 / natural killer cell tolerance induction / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 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-4 production / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / response to interleukin-1 / positive regulation of interleukin-1 beta production / female pregnancy / positive regulation of interleukin-8 production / cellular response to virus / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / chemotaxis / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / positive regulation of NF-kappaB transcription factor activity / carbohydrate binding / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å | |||||||||
Authors | Kishishita, S. / Nishino, A. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: To be Published Title: Crystal structure of N-terminal domain of human galectin-9 containing L-acetyllactosamine Authors: Kishishita, S. / Nishino, A. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yy1.cif.gz | 44.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yy1.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 2yy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/2yy1 ftp://data.pdbj.org/pub/pdb/validation_reports/yy/2yy1 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | This structure indicates monomer structure in this crystal packing. But, there is no experimental evidence. |
-Components
#1: Protein | Mass: 17222.146 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PK060220-05 / Production host: cell-free protein synthesis (unknown) / References: UniProt: O00182 |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-lactosamine |
#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: 1.98 Å3/Da / Density % sol: 37.99 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: 0.2M sodium acetate trihydrate, 0.1M sodium cacodylate, 30% PEG 8000, 30mM L-acetyllactosamine, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9792 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 17, 2006 / Details: mirrors |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 15074 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 12.8989 % / Biso Wilson estimate: 8.4 Å2 / Rsym value: 0.077 / Net I/σ(I): 46.3176 |
Reflection shell | Resolution: 2.15→2.26 Å / Mean I/σ(I) obs: 11.3 / Rsym value: 0.19 / % possible all: 78.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.17→30.81 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 120533.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.0567 Å2 / ksol: 0.421937 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.17→30.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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