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- PDB-2eys: A structural basis for selection and cross-species reactivity of ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2eys | ||||||
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Title | A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition | ||||||
![]() | (NKT15) x 2 | ||||||
![]() | IMMUNE SYSTEM / Natural killer T cell receptor / NKT cell receptor / NKT15 | ||||||
Function / homology | ![]() alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding ...alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / antibacterial humoral response / adaptive immune response / blood microparticle / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kjer-Nielsen, L. / Borg, N.A. | ||||||
![]() | ![]() Title: A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition Authors: Kjer-Nielsen, L. / Borg, N.A. / Pellicci, D.G. / Beddoe, T. / Kostenko, L. / Clements, C.S. / Williamson, N.A. / Smyth, M.J. / Besra, G.S. / Reid, H.H. / Bharadwaj, M. / Godfrey, D.I. / ...Authors: Kjer-Nielsen, L. / Borg, N.A. / Pellicci, D.G. / Beddoe, T. / Kostenko, L. / Clements, C.S. / Williamson, N.A. / Smyth, M.J. / Besra, G.S. / Reid, H.H. / Bharadwaj, M. / Godfrey, D.I. / Rossjohn, J. / McCluskey, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.3 KB | Display | ![]() |
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PDB format | ![]() | 78.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
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Full document | ![]() | 452.8 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2eyrC ![]() 2eytC ![]() 1mi5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 23365.803 Da / Num. of mol.: 1 / Mutation: T164C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein | Mass: 27701.801 Da / Num. of mol.: 1 / Mutation: S174C, C192A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.3 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 9% PEG 3350, 0.1M cacodylate, 0.2M ammonium acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→65.51 Å / Num. obs: 22974 / Observed criterion σ(F): 0 |
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Processing
Software | Name: REFMAC / Version: 5.2.0005 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1MI5 Resolution: 2.21→65.51 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.896 / SU B: 15.858 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 29.463 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→65.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.205→2.262 Å / Total num. of bins used: 20
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