[English] 日本語
![](img/lk-miru.gif)
- PDB-5d4k: Crystal structure of the human polymeric Ig receptor (pIgR) ectodomain -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5d4k | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the human polymeric Ig receptor (pIgR) ectodomain | |||||||||
![]() | Polymeric immunoglobulin receptor | |||||||||
![]() | IMMUNE SYSTEM / Ig Super Family (IgSF) / polymeric Ig-binding protein / mucosal immunity / Secretory Component | |||||||||
Function / homology | ![]() polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / secretory IgA immunoglobulin complex / Fc receptor signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / azurophil granule membrane / receptor clustering / epidermal growth factor receptor signaling pathway / receptor complex ...polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / secretory IgA immunoglobulin complex / Fc receptor signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / azurophil granule membrane / receptor clustering / epidermal growth factor receptor signaling pathway / receptor complex / Neutrophil degranulation / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Stadtmueller, B.M. / Bjorkman, P.J. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: The structure and dynamics of secretory component and its interactions with polymeric immunoglobulins. Authors: Stadtmueller, B.M. / Huey-Tubman, K.E. / Lopez, C.J. / Yang, Z. / Hubbell, W.L. / Bjorkman, P.J. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 398.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 331.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 37.5 KB | Display | |
Data in CIF | ![]() | 52.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5f1sC ![]() 1xedS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||
2 | ![]()
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 2 - 549 / Label seq-ID: 2 - 549
|
-
Components
#1: Protein | Mass: 61483.004 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 19-565) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.38 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M ammonium sulfate, 0.1M BisTris pH 5.5, 31% Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.599→39.623 Å / Num. all: 49242 / Num. obs: 49242 / % possible obs: 96.5 % / Redundancy: 3 % / Biso Wilson estimate: 51.53 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.07 / Rsym value: 0.058 / Net I/av σ(I): 11.696 / Net I/σ(I): 13.7 / Num. measured all: 145998 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1XED Resolution: 2.599→36.984 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 28.17 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 271.63 Å2 / Biso mean: 69.2157 Å2 / Biso min: 22.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.599→36.984 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|