+Open data
-Basic information
Entry | Database: PDB / ID: 2ptv | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of NK cell receptor ligand CD48 | ||||||
Components | CD48 antigen | ||||||
Keywords | IMMUNE SYSTEM / CD48 / NK cell receptor | ||||||
Function / homology | Function and homology information natural killer cell activation involved in immune response / mast cell activation / Cell surface interactions at the vascular wall / MHC class I protein binding / T cell activation / external side of plasma membrane / signal transduction / protein-containing complex / extracellular region Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Deng, L. / Velikovsky, C.A. / Mariuzza, R.A. | ||||||
Citation | Journal: Immunity / Year: 2007 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ptv.cif.gz | 34.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ptv.ent.gz | 23.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ptv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ptv_validation.pdf.gz | 421.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ptv_full_validation.pdf.gz | 421.3 KB | Display | |
Data in XML | 2ptv_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 2ptv_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/2ptv ftp://data.pdbj.org/pub/pdb/validation_reports/pt/2ptv | HTTPS FTP |
-Related structure data
Related structure data | 2pttSC 2ptuC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | The biological assembly is the monomer in the asymmetric unit. |
-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.) Mus musculus (house mouse) / Gene: Cd48, Bcm-1 / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codonPlus-DE3 RIL / References: UniProt: P18181 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.49 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 30% (w/v) PEG 8000, 100 mM sodium imidazole, 0.2 M NaCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
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: 1.66→50 Å / Num. obs: 11309 / % possible obs: 97.3 % / Redundancy: 12.9 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 66.7 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 8.4 / Num. unique all: 1041 / % possible all: 81.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PTT Resolution: 1.66→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.524 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.127 / 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: 25.242 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
|