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Yorodumi- PDB-6y0m: Crystal structure of human CD23 lectin domain N225D, K229E, S252N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y0m | |||||||||
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Title | Crystal structure of human CD23 lectin domain N225D, K229E, S252N, T251N mutant | |||||||||
Components | Low affinity immunoglobulin epsilon Fc receptor membrane-bound form | |||||||||
Keywords | IMMUNE SYSTEM / Antibody receptor / C-type lectin / calcium binding protein / IgE / immunoglobulin E / CD23 | |||||||||
Function / homology | Function and homology information low-affinity IgE receptor activity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / positive regulation of humoral immune response mediated by circulating immunoglobulin / NOTCH2 intracellular domain regulates transcription / macrophage activation / IgE binding / positive regulation of killing of cells of another organism / positive regulation of nitric-oxide synthase biosynthetic process / Interleukin-10 signaling ...low-affinity IgE receptor activity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / positive regulation of humoral immune response mediated by circulating immunoglobulin / NOTCH2 intracellular domain regulates transcription / macrophage activation / IgE binding / positive regulation of killing of cells of another organism / positive regulation of nitric-oxide synthase biosynthetic process / Interleukin-10 signaling / positive regulation of nitric-oxide synthase activity / integrin binding / carbohydrate binding / Interleukin-4 and Interleukin-13 signaling / immune response / external side of plasma membrane / extracellular exosome / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Ilkow, V.F. / Davies, A.M. / Sutton, B.J. / McDonnell, J.M. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Febs Open Bio / Year: 2021 Title: Reviving lost binding sites: Exploring calcium-binding site transitions between human and murine CD23. Authors: Ilkow, V.F. / Davies, A.M. / Dhaliwal, B. / Beavil, A.J. / Sutton, B.J. / McDonnell, J.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y0m.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y0m.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 6y0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/6y0m ftp://data.pdbj.org/pub/pdb/validation_reports/y0/6y0m | HTTPS FTP |
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-Related structure data
Related structure data | 6y0lC 4g9aS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16205.928 Da / Num. of mol.: 1 / Mutation: N225D, K229E, S252N, T251N Source method: isolated from a genetically manipulated source Details: mutations: N225D, K229E, S252N, T251N / Source: (gene. exp.) Homo sapiens (human) / Gene: FCER2, CD23A, CLEC4J, FCE2, IGEBF / Production host: Escherichia coli (E. coli) / References: UniProt: P06734 |
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#2: 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: 2.7 Å3/Da / Density % sol: 54.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M sodium-cacodylate pH 6.5, 1M tri-sodium-citrate Crystals were soaked with a solution of 0.1M sodium-cacodylate at pH 7.1, 1.4M tri-sodium-citrate and 10mM CaCl2 for four days before ...Details: 0.1M sodium-cacodylate pH 6.5, 1M tri-sodium-citrate Crystals were soaked with a solution of 0.1M sodium-cacodylate at pH 7.1, 1.4M tri-sodium-citrate and 10mM CaCl2 for four days before harvesting which also served as a cryoprotectant. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→49.88 Å / Num. obs: 29150 / % possible obs: 99.9 % / Redundancy: 39 % / Biso Wilson estimate: 19.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.018 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 35.5 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.808 / Rpim(I) all: 0.538 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G9A Resolution: 1.5→49.877 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→49.877 Å
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Refine LS restraints |
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LS refinement shell |
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