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Yorodumi- PDB-2xqb: Crystal Structure of anti-IL-15 Antibody in Complex with human IL-15 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xqb | ||||||
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Title | Crystal Structure of anti-IL-15 Antibody in Complex with human IL-15 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / AFFINITY MATURATION | ||||||
Function / homology | Function and homology information NK T cell proliferation / extrathymic T cell selection / positive regulation of protein O-linked glycosylation / natural killer cell proliferation / positive regulation of natural killer cell differentiation / positive regulation of tissue remodeling / natural killer cell differentiation / neutrophil activation / cytokine receptor binding / regulation of defense response to virus by host ...NK T cell proliferation / extrathymic T cell selection / positive regulation of protein O-linked glycosylation / natural killer cell proliferation / positive regulation of natural killer cell differentiation / positive regulation of tissue remodeling / natural killer cell differentiation / neutrophil activation / cytokine receptor binding / regulation of defense response to virus by host / tyrosine phosphorylation of STAT protein / interleukin-15-mediated signaling pathway / Interleukin-15 signaling / positive regulation of natural killer cell proliferation / negative regulation of cold-induced thermogenesis / regulation of T cell differentiation / positive regulation of interleukin-17 production / macrophage differentiation / lymph node development / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of phagocytosis / cell maturation / positive regulation of cytokine production / cytokine activity / positive regulation of inflammatory response / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of immune response / cell-cell signaling / endosome / nuclear speck / immune response / positive regulation of cell population proliferation / Golgi apparatus / signal transduction / extracellular space / extracellular region / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Lowe, D.C. / Gerhardt, S. / Ward, A. / Hargreaves, D. / Anderson, M. / StGallay, S. / Vousden, K. / Ferraro, F. / Pauptit, R.A. / Cochrane, D. ...Lowe, D.C. / Gerhardt, S. / Ward, A. / Hargreaves, D. / Anderson, M. / StGallay, S. / Vousden, K. / Ferraro, F. / Pauptit, R.A. / Cochrane, D. / Pattison, D.V. / Buchanan, C. / Popovic, B. / Finch, D.K. / Wilkinson, T. / Sleeman, M. / Vaughan, T.J. / Cruwys, S. / Mallinder, P.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Engineering a High Affinity Anti-Il-15 Antibody: Crystal Structure Reveals an Alpha-Helix in Vh Cdr3 as Key Component of Paratope. Authors: Lowe, D.C. / Gerhardt, S. / Ward, A. / Hargreaves, D. / Anderson, M. / Ferraro, F. / Pauptit, R.A. / Pattison, D.V. / Buchanan, C. / Popovic, B. / Finch, D.K. / Wilkinson, T. / Sleeman, M. / ...Authors: Lowe, D.C. / Gerhardt, S. / Ward, A. / Hargreaves, D. / Anderson, M. / Ferraro, F. / Pauptit, R.A. / Pattison, D.V. / Buchanan, C. / Popovic, B. / Finch, D.K. / Wilkinson, T. / Sleeman, M. / Vaughan, T.J. / Mallinder, P.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xqb.cif.gz | 216 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xqb.ent.gz | 171.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xqb_validation.pdf.gz | 419.8 KB | Display | wwPDB validaton report |
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Full document | 2xqb_full_validation.pdf.gz | 449.4 KB | Display | |
Data in XML | 2xqb_validation.xml.gz | 16 KB | Display | |
Data in CIF | 2xqb_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/2xqb ftp://data.pdbj.org/pub/pdb/validation_reports/xq/2xqb | HTTPS FTP |
-Related structure data
Related structure data | 1aqkS 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: 12784.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PT7#3.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): STAR / References: UniProt: P40933 | ||
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#2: Antibody | Mass: 25390.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293/EBNA / Production host: Homo sapiens (human) | ||
#3: Antibody | Mass: 22915.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293/EBNA / Production host: Homo sapiens (human) | ||
#4: Chemical | #5: 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: 1.8 Å3/Da / Density % sol: 32 % / Description: NONE |
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Crystal grow | pH: 9.5 Details: PCTP 100MM, PH 9.5, 25 %W/V PEG-3350, 200MM AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Feb 26, 2008 / Details: OSMIC |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→69.7 Å / Num. obs: 17425 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AQK Resolution: 2.6→69.71 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.859 / SU B: 31.94 / SU ML: 0.339 / Cross valid method: THROUGHOUT / ESU R: 2.527 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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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: 51.224 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→69.71 Å
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