+Open data
-Basic information
Entry | Database: PDB / ID: 4msv | ||||||
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Title | Crystal structure of FASL and DcR3 complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / FASL / DCR3 / TNF / TNFR / TNF6 / STRUCTURAL GENOMICS / PSI-BIOLOGY / NEW YORK STRUCTURAL GENOMICS / RESEARCH CONSORTIUM / NYSGRC / IMMUNITY / TNF SUPE CD95L / FAS LIGAND / MEMBRANE / ATOMS-TO-ANIMALS: THE IMMUNE FUNCTION NETWORK / IFN / JELLY-ROLL FOLD / BIND TNF RECEPTOR FAS / Protein Structure Initiative / New York Structural Genomics Research Consortium / CD95L / TNF SUPERFAMILY / SECRETED PROTEIN / CYTOKINE | ||||||
Function / homology | Function and homology information positive regulation of phosphatidylserine exposure on apoptotic cell surface / inflammatory cell apoptotic process / release of sequestered calcium ion into cytosol by endoplasmic reticulum / cytoplasmic vesicle lumen / FasL/ CD95L signaling / intracellular chloride ion homeostasis / retinal cell programmed cell death / TNFs bind their physiological receptors / Regulation by c-FLIP / CASP8 activity is inhibited ...positive regulation of phosphatidylserine exposure on apoptotic cell surface / inflammatory cell apoptotic process / release of sequestered calcium ion into cytosol by endoplasmic reticulum / cytoplasmic vesicle lumen / FasL/ CD95L signaling / intracellular chloride ion homeostasis / retinal cell programmed cell death / 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 / necroptotic signaling pathway / T cell apoptotic process / positive regulation of endothelial cell apoptotic process / response to growth factor / tumor necrosis factor receptor binding / death receptor binding / FOXO-mediated transcription of cell death genes / RIPK1-mediated regulated necrosis / positive regulation of epidermal growth factor receptor signaling pathway / 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 / apoptotic signaling pathway / caveola / cellular response to type II interferon / : / 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 / positive regulation of cell population proliferation / negative regulation of apoptotic process / 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: 2.5 Å | ||||||
Authors | Liu, W. / Ramagopal, U.A. / Zhan, C. / Bonanno, J.B. / Bhosle, R.C. / Nathenson, S.G. / Almo, S.C. / Atoms-to-Animals: The Immune Function Network (IFN) / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
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 | 4msv.cif.gz | 77.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4msv.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 4msv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4msv_validation.pdf.gz | 446.1 KB | Display | wwPDB validaton report |
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Full document | 4msv_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 4msv_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 4msv_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/4msv ftp://data.pdbj.org/pub/pdb/validation_reports/ms/4msv | HTTPS FTP |
-Related structure data
Related structure data | 5l19C 5l36C 4j6gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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 / Plasmid: pMT-Bip-V5-His / Cell line (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: O95407 |
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#2: Protein | Mass: 17344.959 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 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21phys / References: UniProt: P48023 |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 1.46 Å3/Da / Density % sol: 15.86 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.09M Malonic Acid, 0.013M Ammonium Citr Tribasic, 0.006M Succinic Acid, 0.015M DL-Malic Acid, 0.02M Sodium Acetate, 0.025 M Sodium Formate, 0.008 M Ammonium Tartrate Dibasic, Final pH 7.0; ...Details: 0.09M Malonic Acid, 0.013M Ammonium Citr Tribasic, 0.006M Succinic Acid, 0.015M DL-Malic Acid, 0.02M Sodium Acetate, 0.025 M Sodium Formate, 0.008 M Ammonium Tartrate Dibasic, Final pH 7.0; 0.1M HEPES:NaOH pH 7.0, 10% (w/v) PEG MME 5000, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 22326 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.116 / Rsym value: 0.092 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 7 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 2 / Rsym value: 0.773 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4J6G Resolution: 2.5→48.52 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.487 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.19 / 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: 45.065 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48.52 Å
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Refine LS restraints |
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