[English] 日本語
![](img/lk-miru.gif)
- PDB-7al7: The Crystal Structure of Human IL-18 in Complex With Human IL-18 ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7al7 | ||||||
---|---|---|---|---|---|---|---|
Title | The Crystal Structure of Human IL-18 in Complex With Human IL-18 Binding Protein | ||||||
![]() |
| ||||||
![]() | CYTOKINE / decoy receptor / antagonist / complex | ||||||
Function / homology | ![]() interleukin-18 binding / interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / receptor antagonist activity / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation / positive regulation of interleukin-13 production / positive regulation of neuroinflammatory response ...interleukin-18 binding / interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / receptor antagonist activity / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation / positive regulation of interleukin-13 production / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / natural killer cell mediated cytotoxicity / negative regulation of myoblast differentiation / type 2 immune response / natural killer cell activation / sleep / neutrophil activation / Interleukin-1 processing / positive regulation of NK T cell proliferation / Interleukin-37 signaling / triglyceride homeostasis / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of natural killer cell proliferation / T-helper 1 type immune response / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / Interleukin-10 signaling / glutathione transferase / glutathione transferase activity / establishment of skin barrier / Pyroptosis / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / glutathione metabolic process / cytokine activity / cholesterol homeostasis / positive regulation of smooth muscle cell proliferation / cellular response to hydrogen peroxide / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / cell-cell signaling / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / angiogenesis / Interleukin-4 and Interleukin-13 signaling / cell population proliferation / response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / inflammatory response / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Detry, S. / Andries, J. / Bloch, Y. / Clancy, D. / Savvides, S.N. | ||||||
Funding support | European Union, 1items
| ||||||
![]() | ![]() Title: Structural basis of human IL-18 sequestration by the decoy receptor IL-18 binding protein in inflammation and tumor immunity. Authors: Detry, S. / Andries, J. / Bloch, Y. / Gabay, C. / Clancy, D.M. / Savvides, S.N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 179.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 139.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 464.8 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f62S S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18749.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The final protein sequence used for crystallization starts at T30 and ends at D170. The N-terminal RTPmu signal sequence is cleaved during expression. The C-terminal AVI-HIS tag was cleaved ...Details: The final protein sequence used for crystallization starts at T30 and ends at D170. The N-terminal RTPmu signal sequence is cleaved during expression. The C-terminal AVI-HIS tag was cleaved by caspase-3 after the DEVD site. In reference to the native sequence, the final protein sequence starts at Q63 and ends at G194, as it lacks an N-terminal region from T31 to K62. Source: (gene. exp.) ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Protein | Mass: 45695.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at ...Details: The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193 Source: (gene. exp.) ![]() ![]() ![]() Plasmid: pET-42 / Gene: IL18, IGIF, IL1F4 / Details (production host): HIS-GST tag added N-terminally / Production host: ![]() ![]() References: UniProt: P08515, UniProt: Q14116, glutathione transferase | ||||
#3: Sugar | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 18% w/v Polyethylene glycol 8000 Temp details: Room temperature |
---|
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→59.39 Å / Num. obs: 26507 / % possible obs: 98.27 % / Redundancy: 6.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Net I/σ(I): 15.67 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3F62 Resolution: 1.801→59.386 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 39.86 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 184.21 Å2 / Biso mean: 38.4789 Å2 / Biso min: 5.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.801→59.386 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|