+Open data
-Basic information
Entry | Database: PDB / ID: 3b9i | ||||||
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Title | Crystal Structure of mouse GITRL at 2.5 A. | ||||||
Components | GITR ligand | ||||||
Keywords | CYTOKINE / GITRL / Glucocorticoid-Induced TNF Receptor Ligand / UNKNOWN FUNCTION | ||||||
Function / homology | Function and homology information regulation of dendritic cell chemotaxis / negative regulation of T-helper 17 cell lineage commitment / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor binding / positive regulation of monocyte chemotaxis / positive regulation of leukocyte migration / positive regulation of macrophage chemotaxis / regulation of T cell proliferation / T cell proliferation involved in immune response ...regulation of dendritic cell chemotaxis / negative regulation of T-helper 17 cell lineage commitment / TNFs bind their physiological receptors / tumor necrosis factor receptor superfamily binding / tumor necrosis factor receptor binding / positive regulation of monocyte chemotaxis / positive regulation of leukocyte migration / positive regulation of macrophage chemotaxis / regulation of T cell proliferation / T cell proliferation involved in immune response / positive regulation of cell adhesion / regulation of protein-containing complex assembly / positive regulation of tyrosine phosphorylation of STAT protein / tumor necrosis factor-mediated signaling pathway / cytokine activity / positive regulation of inflammatory response / positive regulation of NF-kappaB transcription factor activity / adaptive immune response / cell surface / extracellular space / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.49 Å | ||||||
Authors | Chattopadhyay, K. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Evolution of GITRL immune function: murine GITRL exhibits unique structural and biochemical properties within the TNF superfamily. Authors: Chattopadhyay, K. / Ramagopal, U.A. / Brenowitz, M. / Nathenson, S.G. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b9i.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b9i.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 3b9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/3b9i ftp://data.pdbj.org/pub/pdb/validation_reports/b9/3b9i | HTTPS FTP |
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-Related structure data
Related structure data | 2qdnSC 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: 15011.407 Da / Num. of mol.: 2 / Fragment: TNF homology domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfsf18, Gitrl / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q7TS55 #2: 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: 2.21 Å3/Da / Density % sol: 44.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% Pentaerythritol Ethoxylate(15/4 EO/OH), 0.05M Ammonium Sulfate and 0.05M Bis-Tris (pH 6.5), Vapor diffusion, Sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. all: 9637 / Num. obs: 9637 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.14 / Rsym value: 0.108 / Χ2: 1.174 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.49→2.59 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.2 / Num. unique all: 923 / Rsym value: 0.487 / Χ2: 1.014 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Starting model: 2QDN Resolution: 2.49→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.662 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.681 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.445 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.557 Å / Total num. of bins used: 20
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