+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ptu | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of NK cell receptor 2B4 (CD244) | ||||||
![]() | Natural killer cell receptor 2B4![]() | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() positive regulation of granzyme B production / myeloid dendritic cell activation / natural killer cell activation involved in immune response / Cell surface interactions at the vascular wall / positive regulation of natural killer cell proliferation / positive regulation of inositol phosphate biosynthetic process / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / positive regulation of interleukin-8 production / positive regulation of type II interferon production ...positive regulation of granzyme B production / myeloid dendritic cell activation / natural killer cell activation involved in immune response / Cell surface interactions at the vascular wall / positive regulation of natural killer cell proliferation / positive regulation of inositol phosphate biosynthetic process / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / positive regulation of interleukin-8 production / positive regulation of type II interferon production / ![]() ![]() 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 | ![]() | 94.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 73.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2pttSC ![]() 2ptvC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is one of the monomers in the asymmetric unit. |
-
Components
#1: Protein | ![]() Mass: 12526.927 Da / Num. of mol.: 4 / Fragment: Ig-like 1, D1, CD48-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 71.91 % |
---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.0 M ammonium dihydrogen phosphate, 0.1 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.38→50 Å / Num. obs: 57316 / % possible obs: 85.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 50.5 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.38→2.47 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4034 / % possible all: 60 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2PTT Resolution: 2.38→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.767 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.222 / 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: 47.35 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.381→2.443 Å / Total num. of bins used: 20
|