+Open data
-Basic information
Entry | Database: PDB / ID: 6yio | ||||||
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Title | CRYSTAL STRUCTURE OF FAB RG6292 IN COMPLEX WITH CD25 ECD | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTIBODY / CD25 ECD / FAB RG6292 / IL2Ra | ||||||
Function / homology | Function and homology information regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-2 binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / interleukin-2-mediated signaling pathway / activated T cell proliferation / inflammatory response to antigenic stimulus ...regulation of T cell tolerance induction / interleukin-2 receptor complex / interleukin-2 receptor activity / interleukin-2 binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / interleukin-2-mediated signaling pathway / activated T cell proliferation / inflammatory response to antigenic stimulus / Interleukin-2 signaling / positive regulation of T cell differentiation / activation-induced cell death of T cells / positive regulation of activated T cell proliferation / Interleukin receptor SHC signaling / negative regulation of T cell proliferation / Notch signaling pathway / negative regulation of inflammatory response / RAF/MAP kinase cascade / cell surface receptor signaling pathway / inflammatory response / immune response / external side of plasma membrane / apoptotic process / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Benz, J. / Koll, H. / Leibrock, L. | ||||||
Citation | Journal: Nat Cancer / Year: 2020 Title: CD25-T reg -depleting antibodies preserving IL-2 signaling on effector T cells enhance effector activation and antitumor immunity. Authors: Solomon, I. / Amann, M. / Goubier, A. / Vargas, F.A. / Zervas, D. / Qing, C. / Henry, J.Y. / Ghorani, E. / Akarca, A.U. / Marafioti, T. / Sledzinska, A. / Sunderland, M.W. / Demane, D.F. / ...Authors: Solomon, I. / Amann, M. / Goubier, A. / Vargas, F.A. / Zervas, D. / Qing, C. / Henry, J.Y. / Ghorani, E. / Akarca, A.U. / Marafioti, T. / Sledzinska, A. / Sunderland, M.W. / Demane, D.F. / Clancy, J.R. / Georgiou, A. / Salimu, J. / Merchiers, P. / Brown, M.A. / Flury, R. / Eckmann, J. / Murgia, C. / Sam, J. / Jacobsen, B. / Marrer-Berger, E. / Boetsch, C. / Belli, S. / Leibrock, L. / Benz, J. / Koll, H. / Sutmuller, R. / Peggs, K.S. / Quezada, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yio.cif.gz | 241.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yio.ent.gz | 192.1 KB | Display | PDB format |
PDBx/mmJSON format | 6yio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yio_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 6yio_full_validation.pdf.gz | 442.2 KB | Display | |
Data in XML | 6yio_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 6yio_validation.cif.gz | 41.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/6yio ftp://data.pdbj.org/pub/pdb/validation_reports/yi/6yio | HTTPS FTP |
-Related structure data
Related structure data | 2b5iS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23219.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RA / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01589 |
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#2: Antibody | Mass: 23646.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) |
#3: Antibody | Mass: 23397.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 25% v/v PEG Smear Medium (12.5% w/v PEG 3350, 12.5% w/v PEG 4000, 12.5% w/v PEG 2000, 12.5% w/v PEG 5000 MME) 0.1M SODIUM ACETATE, PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99982 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99982 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→69.98 Å / Num. obs: 56064 / % possible obs: 99.9 % / Redundancy: 3.39 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.83→1.92 Å / Rmerge(I) obs: 0.74 / Num. unique obs: 7407 / CC1/2: 0.656 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B5I Resolution: 1.83→69.98 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.147 / SU Rfree Blow DPI: 0.13 / SU Rfree Cruickshank DPI: 0.125
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Displacement parameters | Biso max: 95.02 Å2 / Biso mean: 33.89 Å2 / Biso min: 16.95 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.83→69.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
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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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