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Open data
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Basic information
Entry | Database: PDB / ID: 5tz2 | |||||||||
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Title | Crystal structure of human CD47 ECD bound to Fab of C47B222 | |||||||||
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![]() | IMMUNE SYSTEM / antigen-Fab complex / immunoglobulin | |||||||||
Function / homology | ![]() cellular response to interleukin-12 / regulation of Fc receptor mediated stimulatory signaling pathway / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / regulation of type II interferon production / ATP export / positive regulation of cell-cell adhesion / cell-cell adhesion mediator activity / regulation of interleukin-10 production / regulation of tumor necrosis factor production ...cellular response to interleukin-12 / regulation of Fc receptor mediated stimulatory signaling pathway / protein binding involved in heterotypic cell-cell adhesion / positive regulation of monocyte extravasation / regulation of type II interferon production / ATP export / positive regulation of cell-cell adhesion / cell-cell adhesion mediator activity / regulation of interleukin-10 production / regulation of tumor necrosis factor production / regulation of interleukin-12 production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / regulation of interleukin-6 production / Signal regulatory protein family interactions / thrombospondin receptor activity / tertiary granule membrane / cellular response to interleukin-1 / Integrin cell surface interactions / specific granule membrane / positive regulation of phagocytosis / positive regulation of stress fiber assembly / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / cellular response to type II interferon / positive regulation of inflammatory response / cell migration / positive regulation of T cell activation / angiogenesis / inflammatory response / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Cardoso, R.M.F. | |||||||||
![]() | ![]() Title: Anti-leukemic activity and tolerability of anti-human CD47 monoclonal antibodies. Authors: Pietsch, E.C. / Dong, J. / Cardoso, R. / Zhang, X. / Chin, D. / Hawkins, R. / Dinh, T. / Zhou, M. / Strake, B. / Feng, P.H. / Rocca, M. / Santos, C.D. / Shan, X. / Danet-Desnoyers, G. / Shi, ...Authors: Pietsch, E.C. / Dong, J. / Cardoso, R. / Zhang, X. / Chin, D. / Hawkins, R. / Dinh, T. / Zhou, M. / Strake, B. / Feng, P.H. / Rocca, M. / Santos, C.D. / Shan, X. / Danet-Desnoyers, G. / Shi, F. / Kaiser, E. / Millar, H.J. / Fenton, S. / Swanson, R. / Nemeth, J.A. / Attar, R.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 226.3 KB | Display | ![]() |
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PDB format | ![]() | 179.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tztC ![]() 5tzuC ![]() 2jjsS C: citing same article ( S: Starting model for refinement |
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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
-Antibody , 3 types, 3 molecules HLC
#1: Antibody | Mass: 24643.623 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 23406.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 14764.539 Da / Num. of mol.: 1 / Fragment: extracellular domain, UNP residues 19-141 / Mutation: C15G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 2 types, 5 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | |
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-Non-polymers , 2 types, 106 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / |
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#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.12 % / Mosaicity: 0.923 ° |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3000, 1M LiCl, 0.1M MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→32.216 Å / Num. obs: 26271 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/av σ(I): 12.794 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.432 / CC1/2: 0.841 / % possible all: 97 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2JJS Resolution: 2.302→32.216 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.2 Å2 / Biso mean: 66.5172 Å2 / Biso min: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.302→32.216 Å
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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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