[English] 日本語
![](img/lk-miru.gif)
- PDB-2ptt: Structure of NK cell receptor 2B4 (CD244) bound to its ligand CD48 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ptt | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of NK cell receptor 2B4 (CD244) bound to its ligand CD48 | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / 2B4 / CD244 / CD48 / NK cell receptor | ||||||
Function / homology | ![]() myeloid dendritic cell activation / natural killer cell activation involved in immune response / mast cell activation / Cell surface interactions at the vascular wall / positive regulation of natural killer cell proliferation / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / T cell activation / adaptive immune response / external side of plasma membrane ...myeloid dendritic cell activation / natural killer cell activation involved in immune response / mast cell activation / Cell surface interactions at the vascular wall / positive regulation of natural killer cell proliferation / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / T cell activation / adaptive immune response / external side of plasma membrane / innate immune response / signal transduction / protein-containing complex / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deng, L. / Velikovsky, C.A. / Mariuzza, R.A. | ||||||
![]() | ![]() Title: Structure of natural killer receptor 2B4 bound to CD48 reveals basis for heterophilic recognition in signaling lymphocyte activation molecule family. Authors: Velikovsky, C.A. / Deng, L. / Chlewicki, L.K. / Fernandez, M.M. / Kumar, V. / Mariuzza, R.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 61.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 447.9 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ptuC ![]() 2ptvC ![]() 1hngS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 12940.734 Da / Num. of mol.: 1 / Fragment: Ig-like C2-type1, D1, 2B4-binding domain / Mutation: T34Y, K52R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 12526.927 Da / Num. of mol.: 1 / Fragment: IG-LIKE 1, D1, CD48-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.25 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6 M ammonium sulfate, 0.1 mM MES, 10% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→50 Å / Num. obs: 28061 / % possible obs: 99.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 53.6 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 8 / Num. unique all: 2733 / % possible all: 97.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HNG Resolution: 1.63→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.712 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.428 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.631→1.674 Å / Total num. of bins used: 20
|