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Yorodumi- PDB-3nfp: Crystal structure of the Fab fragment of therapeutic antibody dac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nfp | ||||||
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Title | Crystal structure of the Fab fragment of therapeutic antibody daclizumab in complex with IL-2Ra (CD25) ectodomain | ||||||
Components |
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Keywords | Immune system/Cytokine / IL-2Ra / CD25 / Daclizumab / Zenapax / therapeutic antibody / immune system / Immune system-Cytokine complex | ||||||
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: 2.86 Å | ||||||
Authors | Yang, H. / Wang, J. / Du, J. / Zhong, C. / Guo, Y. / Ding, J. | ||||||
Citation | Journal: Cell Res. / Year: 2010 Title: Structural basis of immunosuppression by the therapeutic antibody daclizumab Authors: Yang, H. / Wang, J. / Du, J. / Zhong, C. / Zhang, D. / Guo, H. / Guo, Y. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nfp.cif.gz | 393.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nfp.ent.gz | 319.5 KB | Display | PDB format |
PDBx/mmJSON format | 3nfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nfp_validation.pdf.gz | 467.4 KB | Display | wwPDB validaton report |
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Full document | 3nfp_full_validation.pdf.gz | 479.6 KB | Display | |
Data in XML | 3nfp_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 3nfp_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/3nfp ftp://data.pdbj.org/pub/pdb/validation_reports/nf/3nfp | HTTPS FTP |
-Related structure data
Related structure data | 3nfsSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23034.682 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: purchased from Roche, expressed in a mammalian expression system #2: Antibody | Mass: 23134.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: purchased from Roche, expressed in a mammalian expression system #3: Protein | Mass: 25388.348 Da / Num. of mol.: 2 / Fragment: UNP residues 22-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL2RA / Cell line (production host): Hi-5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01589 #4: Water | ChemComp-HOH / | |
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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: 2.54 Å3/Da / Density % sol: 51.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Tris-HCl, 0.2M MgCl2, 10% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jan 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 31671 / % possible obs: 95.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NFS Resolution: 2.86→50 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.857 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 187.67 Å2 / Biso mean: 69.528 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.86→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.863→2.937 Å / Total num. of bins used: 20
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