+Open data
-Basic information
Entry | Database: PDB / ID: 7ra9 | ||||||
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Title | Designed StabIL-2 seq1 | ||||||
Components | Interleukin-2 | ||||||
Keywords | CYTOKINE / synthetic protein | ||||||
Function / homology | Function and homology information 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 ...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 / negative regulation of B cell apoptotic process / Interleukin-2 signaling / positive regulation of immunoglobulin production / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / T cell differentiation / Interleukin receptor SHC signaling / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / 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 adhesion / immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Jude, K.M. / Chu, A.E. / Huang, P.-S. / Garcia, K.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Interleukin-2 superkines by computational design. Authors: Ren, J. / Chu, A.E. / Jude, K.M. / Picton, L.K. / Kare, A.J. / Su, L. / Montano Romero, A. / Huang, P.S. / Garcia, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ra9.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ra9.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ra9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ra9_validation.pdf.gz | 453.4 KB | Display | wwPDB validaton report |
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Full document | 7ra9_full_validation.pdf.gz | 454 KB | Display | |
Data in XML | 7ra9_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 7ra9_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/7ra9 ftp://data.pdbj.org/pub/pdb/validation_reports/ra/7ra9 | HTTPS FTP |
-Related structure data
Related structure data | 7raaC 4nejS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/882 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15133.517 Da / Num. of mol.: 1 Mutation: G27M, I28L, K32D, M39L, E52S, V69A, L72A, Q74G, S75D, K76D, N77P, F78K, H79T, L80I, delta81-82, L85V, I86V, I92F, V115I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P60568 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EPE / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.27 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 0.2 M Li2SO4, 0.1 M CAPS pH 10.5, 1.2 M NaH2PO4, and 0.8 M K2HPO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033167 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40.35 Å / Num. obs: 8217 / % possible obs: 95.97 % / Redundancy: 16.9 % / Biso Wilson estimate: 47.25 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rpim(I) all: 0.07409 / Rrim(I) all: 0.3092 / Rsym value: 0.2997 / Net I/σ(I): 5.78 |
Reflection shell | Resolution: 2.2→2.279 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 0.57 / Num. unique obs: 697 / CC1/2: 0.266 / CC star: 0.648 / Rpim(I) all: 1.141 / Rrim(I) all: 3.606 / Rsym value: 3.411 / % possible all: 78.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NEJ Resolution: 2.2→40.35 Å / SU ML: 0.3426 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.5766 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 / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→40.35 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.0715517893 Å / Origin y: 26.7229094276 Å / Origin z: 118.886961607 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 10 through 135) |