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Yorodumi- PDB-2cdg: Structure and binding kinetics of three different human CD1d-alph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cdg | ||||||
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Title | Structure and binding kinetics of three different human CD1d-alpha- Galactosylceramide-specific T cell receptors (TCR 5B) | ||||||
Components | (TCR 5E) x 2 | ||||||
Keywords | RECEPTOR / CD1D / MHC CLASS I / TCR 5B | ||||||
Function / homology | Function and homology information 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 / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway ...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 / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / immune response / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Gadola, S.D. / Koch, M. / Marles-Wright, J. / Lissin, N.M. / Sheperd, D. / Matulis, G. / Harlos, K. / Villiger, P.M. / Stuart, D.I. / Jakobsen, B.K. ...Gadola, S.D. / Koch, M. / Marles-Wright, J. / Lissin, N.M. / Sheperd, D. / Matulis, G. / Harlos, K. / Villiger, P.M. / Stuart, D.I. / Jakobsen, B.K. / Cerundolo, V. / Jones, E.Y. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2006 Title: Structrue and Binding Kinetics of Three Different Human Cd1D-Alpha-Galactosylceramide-Specific T Cell Receptors Authors: Gadola, S.D. / Koch, M. / Marles-Wright, J. / Lissin, N.M. / Sheperd, D. / Matulis, G. / Harlos, K. / Villiger, P.M. / Stuart, D.I. / Jakobsen, B.K. / Cerundolo, V. / Jones, E.Y. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cdg.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cdg.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 2cdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/2cdg ftp://data.pdbj.org/pub/pdb/validation_reports/cd/2cdg | HTTPS FTP |
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-Related structure data
Related structure data | 2cdeC 2cdfSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 20603.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NON CANONICAL HUMAN NATURAL KILLER (NK) T CELL RECEPTOR 5E NON-VALPHA24 AND VBETA11 Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848*PLUS |
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#2: Protein | Mass: 27651.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NON CANONICAL HUMAN NATURAL KILLER (NK) T CELL RECEPTOR 5E NON-VALPHA24 AND VBETA11 Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01850*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 43 % |
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Crystal grow | Details: 200 MM DI-AMMONIUM TARTRATE, 20 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→18 Å / Num. obs: 13750 / % possible obs: 96.6 % / Observed criterion σ(I): 0.5 / Redundancy: 5.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.6→2.67 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 87.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CDF Resolution: 2.6→61.66 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.825 / SU B: 31.974 / SU ML: 0.332 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / 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: 22.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→61.66 Å
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Refine LS restraints |
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