+Open data
-Basic information
Entry | Database: PDB / ID: 7zmz | ||||||
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Title | Engineered Interleukin 2 bound to CD25 receptor | ||||||
Components |
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Keywords | CYTOKINE / CYTOKINE RECEPTOR / PROTEIN ENGINEERING / SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-2 binding / kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus ...regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-2 binding / kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / activated T cell proliferation / natural killer cell activation / positive regulation of regulatory T cell differentiation / : / kinase activator activity / inflammatory response to antigenic stimulus / negative regulation of B cell apoptotic process / Interleukin-2 signaling / positive regulation of T cell differentiation / positive regulation of immunoglobulin production / positive regulation of dendritic spine development / activation-induced cell death of T cells / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / T cell differentiation / Interleukin receptor SHC signaling / negative regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / Notch signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein phosphorylation / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of type II interferon production / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / positive regulation of cell growth / carbohydrate binding / response to ethanol / adaptive immune response / transcription by RNA polymerase II / cell surface receptor signaling pathway / cell adhesion / inflammatory response / immune response / external side of plasma membrane / apoptotic process / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Fyfe, P.K. / Moraga, I. / Gaggero, S. / Mitra, S. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Sci Immunol / Year: 2022 Title: IL-2 is inactivated by the acidic pH environment of tumors enabling engineering of a pH-selective mutein. Authors: Gaggero, S. / Martinez-Fabregas, J. / Cozzani, A. / Fyfe, P.K. / Leprohon, M. / Yang, J. / Thomasen, F.E. / Winkelmann, H. / Magnez, R. / Conti, A.G. / Wilmes, S. / Pohler, E. / van Gijsel ...Authors: Gaggero, S. / Martinez-Fabregas, J. / Cozzani, A. / Fyfe, P.K. / Leprohon, M. / Yang, J. / Thomasen, F.E. / Winkelmann, H. / Magnez, R. / Conti, A.G. / Wilmes, S. / Pohler, E. / van Gijsel Bonnello, M. / Thuru, X. / Quesnel, B. / Soncin, F. / Piehler, J. / Lindorff-Larsen, K. / Roychoudhuri, R. / Moraga, I. / Mitra, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zmz.cif.gz | 127.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zmz.ent.gz | 94.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zmz_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
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Full document | 7zmz_full_validation.pdf.gz | 446 KB | Display | |
Data in XML | 7zmz_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 7zmz_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/7zmz ftp://data.pdbj.org/pub/pdb/validation_reports/zm/7zmz | HTTPS FTP |
-Related structure data
Related structure data | 2b5iS S: Starting model for refinement |
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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
#1: Protein | Mass: 16821.375 Da / Num. of mol.: 1 / Mutation: T37H, R38L, T41S, F42Y, K43G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60568 |
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#2: Protein | Mass: 29016.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01589 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.59 Å3/Da / Density % sol: 73.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 19% PEG 3350, 0.2 M Sodium tartrate dibasic dihydrate, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→64.33 Å / Num. obs: 9238 / % possible obs: 100 % / Redundancy: 18.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.078 / Rrim(I) all: 0.246 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3.2→3.42 Å / Redundancy: 19.1 % / Rmerge(I) obs: 5.973 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1650 / CC1/2: 0.592 / Rpim(I) all: 1.974 / Rrim(I) all: 6.293 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2b5i Resolution: 3.2→64.3 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 147.06 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→64.3 Å
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Refine LS restraints |
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Refinement TLS params. | Method: refined / Origin x: -3.5108 Å / Origin y: 34.4197 Å / Origin z: 4.3281 Å
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Refinement TLS group | Selection details: all |