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- PDB-1fp5: CRYSTAL STRUCTURE ANALYSIS OF THE HUMAN IGE-FC CEPSILON3-CEPSILON... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fp5 | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF THE HUMAN IGE-FC CEPSILON3-CEPSILON4 FRAGMENT. | ||||||
![]() | IGE HEAVY CHAIN EPSILON-1 | ||||||
![]() | IMMUNE SYSTEM / Antibody / Fc / Immunoglobin fold / "closed" IgE-Fc | ||||||
Function / homology | ![]() adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / type 2 immune response ...adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / type 2 immune response / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / mast cell degranulation / B cell proliferation / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / complement activation, classical pathway / FCERI mediated MAPK activation / antigen binding / B cell receptor signaling pathway / FCERI mediated NF-kB activation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / inflammatory response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wurzburg, B.A. / Garman, S.C. / Jardetzky, T.S. | ||||||
![]() | ![]() Title: Structure of the human IgE-Fc C epsilon 3-C epsilon 4 reveals conformational flexibility in the antibody effector domains. Authors: Wurzburg, B.A. / Garman, S.C. / Jardetzky, T.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.8 KB | Display | ![]() |
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PDB format | ![]() | 42 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.5 KB | Display | ![]() |
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Full document | ![]() | 435.4 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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Unit cell |
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Details | The asymmetric unit contains one chain of the Fc homodimer. The biological dimer can be generated from chain A. |
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Components
#1: Antibody | Mass: 24821.018 Da / Num. of mol.: 1 / Fragment: CEPSILON3-CEPSILON4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 45.5 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 8 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 7, 1999 / Details: 1mm x 1mm slits, 25 m from crystal |
Radiation | Monochromator: Si (111), cryogenically-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.906 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 12322 / Num. obs: 12322 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 33.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 10.6 / Num. unique all: 1208 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. obs: 12340 / Num. measured all: 106855 |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Method to determine structure: ![]() Details: Density for the Cepsilon4 AB loop was particularly poor, especially from residues 453-457, and this region of the loop was built sterically. The B-factors were generally higher and the ...Details: Density for the Cepsilon4 AB loop was particularly poor, especially from residues 453-457, and this region of the loop was built sterically. The B-factors were generally higher and the electron density generally poorer for the BC- DE- and FG-loops of the Cepsilon3 domain that bind to the high affinity receptor. The residue K435 sits at the interdomain interface and the side chain may partially fill a gap in the space between the domains. This is not obvious from the structure, however, as all of the atoms could not be modeled for this residue. The structure contains two cis-Prolines : P471 and P533 There are N-linked carbohydrates attached to the protein at residues N371 and N394. Some electron density is observed for the carbohydrate attached to N394, but no electron density is observed for the carbohydrate attached to N371. Carbohydrates were not modeled in the structure and so they are not present in the PDB file.
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Displacement parameters | Biso mean: 51.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 11053 / σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.242 / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 51.9 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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