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Yorodumi- PDB-5l36: Crystal Structure of a human FasL mutant in complex with human DcR3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l36 | ||||||||||||
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Title | Crystal Structure of a human FasL mutant in complex with human DcR3 | ||||||||||||
Components |
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Keywords | APOPTOSIS / FasL / CD95L / DcR3 / TNF ligand and receptor / decoy receptor | ||||||||||||
Function / homology | Function and homology information release of sequestered calcium ion into cytosol by endoplasmic reticulum / positive regulation of phosphatidylserine exposure on apoptotic cell surface / inflammatory cell apoptotic process / cytoplasmic vesicle lumen / FasL/ CD95L signaling / retinal cell programmed cell death / intracellular chloride ion homeostasis / TNFs bind their physiological receptors / Regulation by c-FLIP / CASP8 activity is inhibited ...release of sequestered calcium ion into cytosol by endoplasmic reticulum / positive regulation of phosphatidylserine exposure on apoptotic cell surface / inflammatory cell apoptotic process / cytoplasmic vesicle lumen / FasL/ CD95L signaling / retinal cell programmed cell death / intracellular chloride ion homeostasis / TNFs bind their physiological receptors / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / endosomal lumen acidification / T cell apoptotic process / necroptotic signaling pathway / response to growth factor / positive regulation of endothelial cell apoptotic process / death receptor binding / tumor necrosis factor receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / RIPK1-mediated regulated necrosis / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / necroptotic process / extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / lysosomal lumen / negative regulation of angiogenesis / cytokine activity / caveola / apoptotic signaling pathway / cellular response to type II interferon / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cell-cell signaling / signaling receptor activity / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / positive regulation of apoptotic process / external side of plasma membrane / signaling receptor binding / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||||||||
Authors | Liu, W. / Bonanno, J.B. / Almo, S.C. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Structure / Year: 2016 Title: Crystal Structure of the Complex of Human FasL and Its Decoy Receptor DcR3. Authors: Liu, W. / Ramagopal, U. / Cheng, H. / Bonanno, J.B. / Toro, R. / Bhosle, R. / Zhan, C. / 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 | 5l36.cif.gz | 73.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l36.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 5l36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/5l36 ftp://data.pdbj.org/pub/pdb/validation_reports/l3/5l36 | HTTPS FTP |
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-Related structure data
Related structure data | 4msvSC 5l19C 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
#1: Protein | Mass: 19044.217 Da / Num. of mol.: 1 / Fragment: UNP residues 30-195 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF6B, DCR3, TR6, UNQ186/PRO212 / Production host: Drosophila (fruit flies) / References: UniProt: O95407 |
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#2: Protein | Mass: 17449.154 Da / Num. of mol.: 1 / Fragment: UNP residues 130-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FASLG, APT1LG1, CD95L, FASL, TNFSF6 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpB1_S (others) References: UniProt: P48023 |
#3: Chemical | ChemComp-NA / |
#4: 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: 4.4 Å3/Da / Density % sol: 72.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M Sodium Acetate:Acetic Acid pH4.5; 1M Ammonium Phosphate Dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jan 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50.01 Å / Num. obs: 11951 / % possible obs: 98.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 3.33 / CC1/2: 0.812 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MSV Resolution: 3.1→50.01 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.905 / SU B: 12.808 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.581 / ESU R Free: 0.317 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 161.72 Å2 / Biso mean: 58.229 Å2 / Biso min: 22.28 Å2
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Refinement step | Cycle: final / Resolution: 3.1→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.099→3.179 Å / Total num. of bins used: 20
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