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Open data
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Basic information
Entry | Database: PDB / ID: 1hxm | ||||||
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Title | Crystal Structure of a Human Vgamma9/Vdelta2 T Cell Receptor | ||||||
![]() | (GAMMA-DELTA T-CELL RECEPTOR) x 2 | ||||||
![]() | IMMUNE SYSTEM / Ig domain / T cell receptor / TCR / gdTCR | ||||||
Function / homology | ![]() gamma-delta T cell receptor complex / gamma-delta T cell activation / T cell receptor complex / plasma membrane => GO:0005886 / positive regulation of phagocytosis / transmembrane signaling receptor activity / positive regulation of T cell activation / T cell receptor signaling pathway / adaptive immune response / immune response ...gamma-delta T cell receptor complex / gamma-delta T cell activation / T cell receptor complex / plasma membrane => GO:0005886 / positive regulation of phagocytosis / transmembrane signaling receptor activity / positive regulation of T cell activation / T cell receptor signaling pathway / adaptive immune response / immune response / external side of plasma membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Allison, T.J. / Winter, C.C. / Fournie, J.J. / Bonneville, M. / Garboczi, D.N. | ||||||
![]() | ![]() Title: Structure of a human gammadelta T-cell antigen receptor. Authors: Allison, T.J. / Winter, C.C. / Fournie, J.J. / Bonneville, M. / Garboczi, D.N. #1: ![]() Title: Peripheral selection of antigen receptor junctional features in a major human gamma delta subset Authors: Davodeau, F. / Peyrat, M.A. / Hallet, M.M. / Houde, I. / Vie, H. / Bonneville, M. #2: ![]() Title: Stimulation of human gamma delta T cells by nonpeptidic mycobaterial ligands Authors: Constant, P. / Davodeau, F. / Peyrat, M.A. / Poquet, Y. / Puzo, G. / Bonneville, M. / Fournie, J.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 | ![]() | 343 KB | Display | ![]() |
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PDB format | ![]() | 288.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.6 KB | Display | ![]() |
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Full document | ![]() | 488.8 KB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 60.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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6 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 25535.939 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 27360.244 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.99 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 28% PEG4000, 0.2 M Li2SO4, 0.1 M Tris-HCl, 20% glycerol, 4 mg/mL protein, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 28, 2000 / Details: Yale mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→60 Å / Num. all: 42118 / Num. obs: 42118 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 59.1 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.7 / % possible all: 97.6 |
Reflection | *PLUS Lowest resolution: 60 Å |
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Processing
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Refinement | Method to determine structure: ![]() Details: Initial model was built into and refined against a 3.25 Angstroms SeMet MAD data set (same space group with very similar unit cell). That model was then brought into this unit cell and ...Details: Initial model was built into and refined against a 3.25 Angstroms SeMet MAD data set (same space group with very similar unit cell). That model was then brought into this unit cell and refined against this 3.12 Angstroms data.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.0227 Å2 / ksol: 0.298879 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.12→30.77 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Weight Biso : 2
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LS refinement shell | Resolution: 3.12→3.32 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 42.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.343 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.29 |