+Open data
-Basic information
Entry | Database: PDB / ID: 3nv1 | ||||||
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Title | Crystal structure of human galectin-9 C-terminal CRD | ||||||
Components | Galectin 9 short isoform variant | ||||||
Keywords | SUGAR BINDING PROTEIN / Sugar Binding | ||||||
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: 1.5 Å | ||||||
Authors | Yoshida, H. / Kamitori, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: X-ray structures of human galectin-9 C-terminal domain in complexes with a biantennary oligosaccharide and sialyllactose Authors: Yoshida, H. / Teraoka, M. / Nishi, N. / Nakakita, S. / Nakamura, T. / Hirashima, M. / Kamitori, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nv1.cif.gz | 45 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nv1.ent.gz | 30.4 KB | Display | PDB format |
PDBx/mmJSON format | 3nv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nv1_validation.pdf.gz | 420.2 KB | Display | wwPDB validaton report |
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Full document | 3nv1_full_validation.pdf.gz | 421.2 KB | Display | |
Data in XML | 3nv1_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 3nv1_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/3nv1 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/3nv1 | HTTPS FTP |
-Related structure data
Related structure data | 3nv2C 3nv3C 3nv4C 3koe C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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Details | AUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN. |
-Components
#1: Protein | Mass: 15729.982 Da / Num. of mol.: 1 Fragment: C-terminal carbohydrate recognition domain, residues 186-323 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53FQ0, UniProt: O00182*PLUS |
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#2: Chemical | ChemComp-NI / |
#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: 2.29 Å3/Da / Density % sol: 46.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG MME 2000, 0.1M Tris pH 8.5, 0.01M nickel chloride hexahydrate, 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: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 22811 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.3 / Num. measured all: 105029 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.96 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3KOE 3koe Resolution: 1.5→26.1 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 83684.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.6762 Å2 / ksol: 0.377788 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→26.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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