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- PDB-3pp4: Epitope characterization and crystal structure of GA101 provide i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pp4 | ||||||
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Title | Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for the type I / type II distinction of anti- CD20 antibodies | ||||||
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![]() | IMMUNE SYSTEM / antibody Fab fragment Ig-domain / CD20 / cyclic peptide / antibody antigen | ||||||
Function / homology | ![]() store-operated calcium entry / positive regulation of calcium ion import across plasma membrane / calcium ion import into cytosol / epidermal growth factor receptor binding / B cell activation / B cell proliferation / plasma membrane raft / immunoglobulin binding / humoral immune response / B cell differentiation ...store-operated calcium entry / positive regulation of calcium ion import across plasma membrane / calcium ion import into cytosol / epidermal growth factor receptor binding / B cell activation / B cell proliferation / plasma membrane raft / immunoglobulin binding / humoral immune response / B cell differentiation / protein tetramerization / B cell receptor signaling pathway / response to bacterium / MHC class II protein complex binding / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hopfner, K.-P. / Lammens, A. | ||||||
![]() | ![]() Title: Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for type I/II distinction of CD20 antibodies. Authors: Niederfellner, G. / Lammens, A. / Mundigl, O. / Georges, G.J. / Schaefer, W. / Schwaiger, M. / Franke, A. / Wiechmann, K. / Jenewein, S. / Slootstra, J.W. / Timmerman, P. / Brannstrom, A. / ...Authors: Niederfellner, G. / Lammens, A. / Mundigl, O. / Georges, G.J. / Schaefer, W. / Schwaiger, M. / Franke, A. / Wiechmann, K. / Jenewein, S. / Slootstra, J.W. / Timmerman, P. / Brannstrom, A. / Lindstrom, F. / Mossner, E. / Umana, P. / Hopfner, K.P. / Klein, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.1 KB | Display | ![]() |
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PDB format | ![]() | 188.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3pp3SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23969.881 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23964.822 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 2852.051 Da / Num. of mol.: 1 / Fragment: large extracellular loop (UNP residues 163-187) / Source method: obtained synthetically / Details: CD20 / Source: (synth.) ![]() |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 16% (w/v) PEG4000, 4% (v/v) isopropanol, 0.1 M sodium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2008 |
Radiation | Monochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 61332 / Num. obs: 60342 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.055 / Rsym value: 0.043 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.21 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PP3 Resolution: 1.6→42.95 Å / SU ML: 0.17 / σ(F): 1.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.508 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6→42.95 Å
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Refine LS restraints |
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LS refinement shell |
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