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Yorodumi- PDB-1j87: HUMAN HIGH AFFINITY FC RECEPTOR FC(EPSILON)RI(ALPHA), HEXAGONAL C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j87 | |||||||||
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Title | HUMAN HIGH AFFINITY FC RECEPTOR FC(EPSILON)RI(ALPHA), HEXAGONAL CRYSTAL FORM 1 | |||||||||
Components | HIGH AFFINITY IMMUNOGLOBULIN EPSILON RECEPTOR ALPHA-SUBUNIT | |||||||||
Keywords | IMMUNE SYSTEM / Fc Receptor / IgE receptor / Glycoprotein | |||||||||
Function / homology | Function and homology information high-affinity IgE receptor activity / type I hypersensitivity / eosinophil degranulation / IgE binding / type 2 immune response / Fc epsilon receptor (FCERI) signaling / mast cell degranulation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization ...high-affinity IgE receptor activity / type I hypersensitivity / eosinophil degranulation / IgE binding / type 2 immune response / Fc epsilon receptor (FCERI) signaling / mast cell degranulation / immunoglobulin mediated immune response / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization / FCERI mediated MAPK activation / FCERI mediated NF-kB activation / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | |||||||||
Authors | Garman, S.C. / Sechi, S. / Kinet, J.P. / Jardetzky, T.S. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The analysis of the human high affinity IgE receptor Fc epsilon Ri alpha from multiple crystal forms. Authors: Garman, S.C. / Sechi, S. / Kinet, J.P. / Jardetzky, T.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j87.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j87.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 1j87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/1j87 ftp://data.pdbj.org/pub/pdb/validation_reports/j8/1j87 | HTTPS FTP |
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-Related structure data
Related structure data | 1j86C 1j88C 1j89C 1f2qS 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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1 |
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Unit cell |
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Details | The biological assembly is a protein monomer with attached carbohydrate |
-Components
#1: Protein | Mass: 19940.119 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR FRAGMENT / Mutation: I170C Source method: isolated from a genetically manipulated source Details: GLYCOSYLATED PROTEIN / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P12319 | ||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #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: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 4000, Sodium Citrate, Sodium Chloride, HECAMEG, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 293K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / pH: 8.5 / Details: Garman, S.C., (2000) Nature, 406, 259. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.004 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 15, 1997 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.004 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. all: 4076 / Num. obs: 4076 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 78.1 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.516 / % possible all: 95.4 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 93.2 % / Num. measured all: 32661 |
Reflection shell | *PLUS % possible obs: 95.4 % / Mean I/σ(I) obs: 5.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1F2Q Resolution: 3.2→19.23 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 1638969.31 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: no density appears for residues 33-35; they are not included in the model
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 13.72 Å2 / ksol: 0.25 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 96 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→19.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.2 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 96 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.393 / % reflection Rfree: 10 % / Rfactor Rwork: 0.32 |