+
Open data
-
Basic information
Entry | Database: PDB / ID: 1d0g | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF DEATH RECEPTOR 5 (DR5) BOUND TO APO2L/TRAIL | ||||||
![]() |
| ||||||
![]() | APOPTOSIS / BINDING AND SPECIFICITY / LIGAND-RECEPTOR COMPLEX / TNF RECEPTOR FAMILY | ||||||
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 | ![]() ![]() | ||||||
![]() | Hymowitz, S.G. / Christinger, H.W. / Fuh, G. / O'Connell, M.P. / Kelley, R.F. / Ashkenazi, A. / de Vos, A.M. | ||||||
![]() | ![]() Title: Triggering cell death: the crystal structure of Apo2L/TRAIL in a complex with death receptor 5. Authors: Hymowitz, S.G. / Christinger, H.W. / Fuh, G. / Ultsch, M. / O'Connell, M. / Kelley, R.F. / Ashkenazi, A. / de Vos, A.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 167 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 138.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 453.2 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is s heterohexamer constructucted of a trimer of chains A,B, and D. Chains R,S,T bind to the interfaces between chains A,B,D. |
-
Components
#1: Protein | Mass: 14578.320 Da / Num. of mol.: 3 / Fragment: EXTRACELLULAR DOMAIN RESIDUES 1-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 19520.852 Da / Num. of mol.: 3 / Fragment: RESIDUES 114-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% Peg8K, 10% ethylene glycol, 0.2M ammonium sulface, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 19K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 152986 / Num. obs: 38908 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.49→2.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.396 / Num. unique all: 3833 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 152986 |
Reflection shell | *PLUS % possible obs: 99.7 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→30 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0.2 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: used maximum likelihood target
| ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.6 Å2
| ||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / σ(F): 0.2 / % reflection Rfree: 9.8 % / Rfactor obs: 0.222 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 47.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.35 / % reflection Rfree: 0.4 % / Rfactor Rwork: 0.319 |