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- PDB-5cir: Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5cir | ||||||
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Title | Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10) | ||||||
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![]() | APOPTOSIS / binding and specificity / ligand-receptor complex / TNF receptor family | ||||||
Function / homology | ![]() TRAIL binding / death receptor activity / 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 / tumor necrosis factor receptor binding ...TRAIL binding / death receptor activity / 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 / tumor necrosis factor receptor binding / regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of extrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Death Receptors and Ligands / RIPK1-mediated regulated necrosis / leukocyte migration / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / transcription factor binding / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway / cytokine activity / Cell surface interactions at the vascular wall / response to insulin / cellular response to mechanical stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / cell-cell signaling / signaling receptor activity / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / protease binding / membrane => GO:0016020 / cell surface receptor signaling pathway / immune response / positive regulation of apoptotic process / membrane raft / signaling receptor binding / apoptotic process / Golgi apparatus / cell surface / signal transduction / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sheriff, S. | ||||||
![]() | ![]() Title: The structure of the death receptor 4-TNF-related apoptosis-inducing ligand (DR4-TRAIL) complex. Authors: Ramamurthy, V. / Yamniuk, A.P. / Lawrence, E.J. / Yong, W. / Schneeweis, L.A. / Cheng, L. / Murdock, M. / Corbett, M.J. / Doyle, M.L. / Sheriff, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.3 KB | Display | ![]() |
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PDB format | ![]() | 119.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.1 KB | Display | ![]() |
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Full document | ![]() | 475.9 KB | Display | |
Data in XML | ![]() | 25.9 KB | Display | |
Data in CIF | ![]() | 35.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 19652.049 Da / Num. of mol.: 3 / Fragment: Residues 114-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11749.284 Da / Num. of mol.: 3 / Fragment: Extracellular domain residues 125-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100 mM MMT (1:2:2 ratio of DL-malic acid, MES, Tris base), pH 5.0, 22.2%(W/V) PEG 2000MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 16742 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 71.79 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 6.4 / Rejects: 0 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: TRAIL FROM 1D0G AND DR4 FROM 1DOG DR5 Resolution: 3→27.6 Å / Cor.coef. Fo:Fc: 0.9265 / Cor.coef. Fo:Fc free: 0.8932 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.372 Details: Non-crystallographic symmetry was used in the form of Local Structure Similarity Restraints (LSSR) with automatic pruning of discrepant residues and with a TARGET_WEIGHT OF 0.5.
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Displacement parameters | Biso max: 135.15 Å2 / Biso mean: 42.22 Å2 / Biso min: 7.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.309 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→27.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.21 Å / Total num. of bins used: 8
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