+Open data
-Basic information
Entry | Database: PDB / ID: 8q5r | ||||||
---|---|---|---|---|---|---|---|
Title | HpARI bound to mouse IL-33 | ||||||
Components |
| ||||||
Keywords | IMMUNOSUPPRESSANT / Helminth / IL-33 / anti-allergy / anti-inflammatory | ||||||
Function / homology | Function and homology information regulation of response to cytokine stimulus / interleukin-33 binding / Interleukin-33 signaling / interleukin-33 receptor binding / negative regulation of macrophage proliferation / positive regulation of CD86 production / positive regulation of CD80 production / positive regulation of cellular defense response / regulation of cytokine activity / positive regulation of MHC class I biosynthetic process ...regulation of response to cytokine stimulus / interleukin-33 binding / Interleukin-33 signaling / interleukin-33 receptor binding / negative regulation of macrophage proliferation / positive regulation of CD86 production / positive regulation of CD80 production / positive regulation of cellular defense response / regulation of cytokine activity / positive regulation of MHC class I biosynthetic process / negative regulation of T-helper 1 type immune response / negative regulation of immunoglobulin production / microglial cell activation involved in immune response / negative regulation of leukocyte migration / PIP3 activates AKT signaling / regulation of sensory perception of pain / microglial cell proliferation / interleukin-33-mediated signaling pathway / positive regulation of type 2 immune response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / response to host immune response / positive regulation of interleukin-5 production / positive regulation of interleukin-13 production / Ub-specific processing proteases / macrophage activation involved in immune response / positive regulation of macrophage activation / positive regulation of MHC class II biosynthetic process / positive regulation of immunoglobulin production / positive regulation of oligodendrocyte differentiation / positive regulation of interleukin-4 production / positive regulation of nitric-oxide synthase biosynthetic process / negative regulation of type II interferon production / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / transport vesicle / positive regulation of cytokine production / cytokine activity / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / chromosome / defense response to virus / intracellular membrane-bounded organelle / host cell nucleus / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / extracellular region / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Heligmosomoides bakeri (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Jamwal, A. / Higgins, M.K. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: To Be Published Title: Structural basis for IL-33 recognition and its antagonism by the helminth effector protein HpARI2 Authors: Jamwal, A. / Higgins, M.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8q5r.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8q5r.ent.gz | 111.2 KB | Display | PDB format |
PDBx/mmJSON format | 8q5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/8q5r ftp://data.pdbj.org/pub/pdb/validation_reports/q5/8q5r | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 17569.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il33 / Production host: Homo sapiens (human) / References: UniProt: Q8BVZ5 | ||||||
---|---|---|---|---|---|---|---|
#2: Protein | Mass: 25876.572 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Heligmosomoides bakeri (invertebrata) / Gene: ARI / Production host: Homo sapiens (human) / References: UniProt: A0A3P7XL18 | ||||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.83 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 6.8 and 22% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 29, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.26 Å / Num. obs: 19343 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.998 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.1→2.14 Å / Num. unique obs: 1046 / CC1/2: 0.728 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.26 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.82 / 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: 160.48 Å2 / Biso mean: 62.4777 Å2 / Biso min: 27.03 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→48.26 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 10.4685 Å / Origin y: -3.6637 Å / Origin z: -12.1678 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|