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Yorodumi- PDB-2cde: Structure and binding kinetics of three different human CD1d-alph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cde | ||||||
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Title | Structure and binding kinetics of three different human CD1d-alpha- Galactosylceramide specific T cell receptors - iNKT-TCR | ||||||
Components | (INKT-TCR) x 2 | ||||||
Keywords | CELL RECEPTOR / T CELL RECEPTOR / TCR / NATURAL KILLER T CELL / CD1D / ALPHA- GALACTOSYLCERAMIDE / MHC CLASS I | ||||||
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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response ...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 / 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: 3.5 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 | 2cde.cif.gz | 261.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cde.ent.gz | 213.4 KB | Display | PDB format |
PDBx/mmJSON format | 2cde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cde_validation.pdf.gz | 478.7 KB | Display | wwPDB validaton report |
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Full document | 2cde_full_validation.pdf.gz | 562.8 KB | Display | |
Data in XML | 2cde_validation.xml.gz | 56.8 KB | Display | |
Data in CIF | 2cde_validation.cif.gz | 75.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/2cde ftp://data.pdbj.org/pub/pdb/validation_reports/cd/2cde | HTTPS FTP |
-Related structure data
Related structure data | 2cdfC 2cdgC 1mi5S 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Antibody | Mass: 21345.570 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: HUMAN INVARIANT NATURAL KILLER T CELL RECEPTOR VALPHA 24 AND VBETA11 Source: (gene. exp.) HOMO SAPIENS (human) / Cell: NATURAL KILLER T CELL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) #2: Protein | Mass: 27702.627 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: HUMAN INVARIANT NATURAL KILLER T CELL RECEPTOR VALPHA 24 AND VBETA11 Source: (gene. exp.) HOMO SAPIENS (human) / Cell: NATURAL KILLER T CELL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01850*PLUS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 61.99 % |
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Crystal grow | Details: 0.5 M NACL, 11 % PEG 8000, 50 MM HEPES PH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 2, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→30 Å / Num. obs: 23622 / % possible obs: 98.1 % / Observed criterion σ(I): 0.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 3.5→3.62 Å / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.4 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MI5 Resolution: 3.5→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.5 / Stereochemistry target values: RESIDUAL
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Solvent computation | Bsol: 80 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.66 Å / Total num. of bins used: 8
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Xplor file |
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