[English] 日本語
Yorodumi- PDB-5m5e: Crystal structure of a interleukin-2 variant in complex with inte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m5e | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a interleukin-2 variant in complex with interleukin-2 receptor | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / Interleukine-2 / interleukine-2 receptor / cytokine / interleukine-2 variant | |||||||||
Function / homology | Function and homology information mature B cell differentiation / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-15 receptor activity / interleukin-7-mediated signaling pathway / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation ...mature B cell differentiation / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-15 receptor activity / interleukin-7-mediated signaling pathway / interleukin-2 binding / CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / response to tacrolimus / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / positive regulation of tissue remodeling / positive regulation of T cell differentiation in thymus / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-4-mediated signaling pathway / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / interleukin-2-mediated signaling pathway / cellular homeostasis / activated T cell proliferation / natural killer cell activation / interleukin-15-mediated signaling pathway / kinase activator activity / positive regulation of regulatory T cell differentiation / : / STAT3 nuclear events downstream of ALK signaling / Interleukin-15 signaling / negative regulation of B cell apoptotic process / Interleukin-2 signaling / cytokine receptor activity / positive regulation of immunoglobulin production / positive regulation of B cell differentiation / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / cytokine binding / T cell differentiation / immunoglobulin mediated immune response / Interleukin receptor SHC signaling / coreceptor activity / positive regulation of B cell proliferation / positive regulation of phagocytosis / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of tyrosine phosphorylation of STAT protein / Interleukin-7 signaling / negative regulation of protein phosphorylation / cytokine activity / growth factor activity / cytokine-mediated signaling pathway / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of type II interferon production / cell-cell signaling / gene expression / positive regulation of cytosolic calcium ion concentration / T cell differentiation in thymus / RAF/MAP kinase cascade / positive regulation of cell growth / carbohydrate binding / protein-containing complex assembly / Interleukin-4 and Interleukin-13 signaling / response to ethanol / adaptive immune response / transcription by RNA polymerase II / receptor complex / cell adhesion / endosome / immune response / external side of plasma membrane / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / cell surface / signal transduction / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Klein, C. / Freimoser-Grundschober, A. / Waldhauer, I. / Stihle, M. / Birk, M. / Benz, J. | |||||||||
Citation | Journal: Oncoimmunology / Year: 2017 Title: Cergutuzumab amunaleukin (CEA-IL2v), a CEA-targeted IL-2 variant-based immunocytokine for combination cancer immunotherapy: Overcoming limitations of aldesleukin and conventional IL-2-based immunocytokines. Authors: Klein, C. / Waldhauer, I. / Nicolini, V.G. / Freimoser-Grundschober, A. / Nayak, T. / Vugts, D.J. / Dunn, C. / Bolijn, M. / Benz, J. / Stihle, M. / Lang, S. / Roemmele, M. / Hofer, T. / van ...Authors: Klein, C. / Waldhauer, I. / Nicolini, V.G. / Freimoser-Grundschober, A. / Nayak, T. / Vugts, D.J. / Dunn, C. / Bolijn, M. / Benz, J. / Stihle, M. / Lang, S. / Roemmele, M. / Hofer, T. / van Puijenbroek, E. / Wittig, D. / Moser, S. / Ast, O. / Brunker, P. / Gorr, I.H. / Neumann, S. / de Vera Mudry, M.C. / Hinton, H. / Crameri, F. / Saro, J. / Evers, S. / Gerdes, C. / Bacac, M. / van Dongen, G. / Moessner, E. / Umana, P. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5m5e.cif.gz | 241.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5m5e.ent.gz | 193.5 KB | Display | PDB format |
PDBx/mmJSON format | 5m5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/5m5e ftp://data.pdbj.org/pub/pdb/validation_reports/m5/5m5e | HTTPS FTP |
---|
-Related structure data
Related structure data | 2erjS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 3 types, 3 molecules BCD
#1: Protein | Mass: 26638.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RB / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P14784 |
---|---|
#2: Protein | Mass: 30220.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RG / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P31785 |
#3: Protein | Mass: 18182.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P60568*PLUS |
-Sugars , 5 types, 7 molecules
#4: Polysaccharide | #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #6: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-MAN / | #10: Sugar | |
---|
-Non-polymers , 3 types, 177 molecules
#8: Chemical | ChemComp-SO4 / #9: Chemical | ChemComp-CYS / | #11: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.25 Å3/Da / Density % sol: 71.09 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES, pH 7.0, 2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→111.07 Å / Num. obs: 55462 / % possible obs: 99.7 % / Redundancy: 10.1 % / Rsym value: 0.17 / Net I/σ(I): 8.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2erj Resolution: 2.3→111.07 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.001 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.882 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→111.07 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|