+Open data
-Basic information
Entry | Database: PDB / ID: 7ox4 | ||||||
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Title | Mouse interleukin-9 in complex with Fab 35D8. | ||||||
Components |
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Keywords | CYTOKINE / IL-9 / Fab | ||||||
Function / homology | Function and homology information interleukin-9 receptor binding / Interleukin-9 signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of interleukin-5 production / regulation of receptor signaling pathway via JAK-STAT / B cell proliferation / immunoglobulin mediated immune response / regulation of peptidyl-tyrosine phosphorylation / B cell differentiation / cytokine activity ...interleukin-9 receptor binding / Interleukin-9 signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of interleukin-5 production / regulation of receptor signaling pathway via JAK-STAT / B cell proliferation / immunoglobulin mediated immune response / regulation of peptidyl-tyrosine phosphorylation / B cell differentiation / cytokine activity / growth factor activity / positive regulation of cell growth / extracellular space Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | De Vos, T. / Savvides, S.N. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Biorxiv / Year: 2022 Title: Structural basis for the mechanism and antagonism of receptor signaling mediated by Interleukin-9 (IL-9) Authors: De Vos, T. / Godar, M. / Bick, F. / Papageorgiou, A.C. / Evangelidis, T. / Markovic, I. / Mortier, E. / Dumoutier, L. / Tripsianes, K. / Blanchetot, C. / Savvides, S.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ox4.cif.gz | 231.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ox4.ent.gz | 183.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ox4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/7ox4 ftp://data.pdbj.org/pub/pdb/validation_reports/ox/7ox4 | HTTPS FTP |
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-Related structure data
Related structure data | 7ox1C 7ox2C 7ox3C 7ox5C 7ox6C 4zs7S 5bv7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 14597.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il9 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15247 |
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-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 24150.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 22446.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
-Non-polymers , 3 types, 330 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Zinc acetate, 23% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 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→48.02 Å / Num. obs: 49669 / % possible obs: 99.7 % / Redundancy: 5.8 % / CC1/2: 0.997 / Net I/σ(I): 9.49 |
Reflection shell | Resolution: 1.8→1.91 Å / Num. unique obs: 7855 / CC1/2: 0.443 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZS7, 5BV7 Resolution: 1.8→48.02 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.15 Å2 / Biso mean: 40.6289 Å2 / Biso min: 14.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→48.02 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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