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Open data
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Basic information
Entry | Database: PDB / ID: 6wl4 | ||||||
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Title | preTCRbeta-pMHC complex crystal structure | ||||||
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![]() | IMMUNE SYSTEM / preTCR / H-2Kb / T cell development / beta selection | ||||||
Function / homology | ![]() RNA replication / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / viral transcription ...RNA replication / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / helical viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / viral transcription / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / MHC class I protein complex / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / negative regulation of neuron projection development / viral nucleocapsid / host cell cytoplasm / defense response to bacterium / ribonucleoprotein complex / external side of plasma membrane / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, X. / Mallis, R.J. / Mizsei, R. / Tan, K. / Reinherz, E.L. / Wang, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Pre-T cell receptors topologically sample self-ligands during thymocyte beta-selection. Authors: Li, X. / Mizsei, R. / Tan, K. / Mallis, R.J. / Duke-Cohan, J.S. / Akitsu, A. / Tetteh, P.W. / Dubey, A. / Hwang, W. / Wagner, G. / Lang, M.J. / Arthanari, H. / Wang, J.H. / Reinherz, E.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 525.4 KB | Display | ![]() |
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PDB format | ![]() | 440.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6wl2C ![]() 6wl3C ![]() 7ji2C ![]() 1nfdS ![]() 1pkuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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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Components
#1: Protein | Mass: 21319.590 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 956.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Protein | Mass: 27350.561 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.17 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.100 M Bicine pH 9.5, 15% (w/v)PEG 20000 / PH range: 6.5-9.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.6→50 Å / Num. obs: 23600 / % possible obs: 99.1 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.099 / Rrim(I) all: 0.298 / Χ2: 0.779 / Net I/σ(I): 2.3 / Num. measured all: 204887 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PKU, 1NFD Resolution: 3.6→49.44 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 225.98 Å2 / Biso mean: 107.4094 Å2 / Biso min: 47.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.6→49.44 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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