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- PDB-4ki1: Primitive triclinic crystal form of the human IgE-Fc(epsilon)3-4 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ki1 | |||||||||
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Title | Primitive triclinic crystal form of the human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23 | |||||||||
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![]() | IMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / LECTIN / ANTIBODY RECEPTOR | |||||||||
Function / homology | ![]() low-affinity IgE receptor activity / IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / type I hypersensitivity / 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 / eosinophil degranulation ...low-affinity IgE receptor activity / IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / type I hypersensitivity / 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 / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / IgE binding / type 2 immune response / positive regulation of killing of cells of another organism / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / mast cell degranulation / B cell proliferation / positive regulation of nitric-oxide synthase biosynthetic process / Interleukin-10 signaling / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / positive regulation of nitric-oxide synthase activity / complement activation, classical pathway / FCERI mediated MAPK activation / antigen binding / B cell receptor signaling pathway / FCERI mediated NF-kB activation / integrin binding / antibacterial humoral response / carbohydrate binding / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / inflammatory response / immune response / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dhaliwal, B. / Pang, M.O.Y. / Sutton, B.J. / Beavil, A.J. | |||||||||
![]() | ![]() Title: A range of C3-C4 interdomain angles in IgE Fc accommodate binding to its receptor CD23. Authors: Dhaliwal, B. / Pang, M.O. / Yuan, D. / Beavil, A.J. / Sutton, B.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 572.9 KB | Display | ![]() |
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PDB format | ![]() | 477.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 48.2 KB | Display | |
Data in CIF | ![]() | 64.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ezmS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24920.146 Da / Num. of mol.: 4 / Fragment: HUMAN IGE-FC(EPSILON)3-4, UNP residues 209-428 / Mutation: N252Q, N264Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 16164.986 Da / Num. of mol.: 4 / Fragment: HUMAN DERCD23, UNP residues 156-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 26 % (w/v) PEG 1,500 and 20 % (v/v) glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→80.4 Å / Num. all: 31141 / Num. obs: 30145 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 61.53 Å2 |
Reflection shell | Resolution: 3.2→3.37 Å / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4EZM Resolution: 3.2→80.4 Å / Cor.coef. Fo:Fc: 0.8409 / Cor.coef. Fo:Fc free: 0.7907 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 79.91 Å2
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Refine analyze | Luzzati coordinate error obs: 0.752 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→80.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å / Total num. of bins used: 15
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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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