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- PDB-4n90: Crystal structure of ternary complex of TRAIL, DR5, and Fab fragm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4n90 | ||||||
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Title | Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody | ||||||
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![]() | Apoptosis/Immune System / DR5 / TRAIL / Agonist / antibody / cooperation / clustering / Apoptosis-Immune System complex | ||||||
Function / homology | ![]() TRAIL receptor activity / TRAIL binding / TRAIL signaling / TRAIL-activated apoptotic signaling pathway / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / activation of NF-kappaB-inducing kinase activity / defense response to tumor cell ...TRAIL receptor activity / TRAIL binding / TRAIL signaling / TRAIL-activated apoptotic signaling pathway / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / Caspase activation via Death Receptors in the presence of ligand / activation of NF-kappaB-inducing kinase activity / defense response to tumor cell / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Death Receptors and Ligands / RIPK1-mediated regulated necrosis / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to endoplasmic reticulum stress / cytokine activity / Cell surface interactions at the vascular wall / response to insulin / cellular response to mechanical stimulus / male gonad development / cell-cell signaling / signaling receptor activity / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / immune response / positive regulation of apoptotic process / signaling receptor binding / apoptotic process / cell surface / signal transduction / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, X. | ||||||
![]() | ![]() Title: Apo2L/TRAIL and the Death Receptor 5 Agonist Antibody AMG 655 Cooperate to Promote Receptor Clustering and Antitumor Activity. Authors: Graves, J.D. / Kordich, J.J. / Huang, T.H. / Piasecki, J. / Bush, T.L. / Sullivan, T. / Foltz, I.N. / Chang, W. / Douangpanya, H. / Dang, T. / O'Neill, J.W. / Mallari, R. / Zhao, X. / ...Authors: Graves, J.D. / Kordich, J.J. / Huang, T.H. / Piasecki, J. / Bush, T.L. / Sullivan, T. / Foltz, I.N. / Chang, W. / Douangpanya, H. / Dang, T. / O'Neill, J.W. / Mallari, R. / Zhao, X. / Branstetter, D.G. / Rossi, J.M. / Long, A.M. / Huang, X. / Holland, P.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 398.8 KB | Display | ![]() |
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PDB format | ![]() | 334.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 540.2 KB | Display | ![]() |
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Full document | ![]() | 629 KB | Display | |
Data in XML | ![]() | 77.9 KB | Display | |
Data in CIF | ![]() | 105.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14193.850 Da / Num. of mol.: 3 / Fragment: UNP residues 57-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: TNFRSF10B, DR5, KILLER, TRAILR2, TRICK2, ZTNFR9, UNQ160/PRO186 Production host: ![]() ![]() #2: Protein | Mass: 19520.852 Da / Num. of mol.: 3 / Fragment: UNP residues 114-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | Mass: 23414.953 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #4: Antibody | Mass: 23774.559 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #5: Chemical | ChemComp-ZN / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris pH 8.0, 1.0 M LiCl, 0.2 M MnCl2, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 63798 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.166 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 3.3→50 Å
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