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Open data
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Basic information
Entry | Database: PDB / ID: 3tpu | ||||||
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Title | 42F3 p5E8/H2-Ld complex | ||||||
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![]() | IMMUNE SYSTEM / IG MHC / Antigen Recognition / TCR-pMHC / chimera protein / Membrane Receptor | ||||||
Function / homology | ![]() antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / defense response / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / immune response / external side of plasma membrane ...antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / defense response / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / immune response / external side of plasma membrane / signaling receptor binding / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Adams, J.J. / Kranz, D.M. / Garcia, K.C. | ||||||
![]() | ![]() Title: T cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex. Authors: Adams, J.J. / Narayanan, S. / Liu, B. / Birnbaum, M.E. / Kruse, A.C. / Bowerman, N.A. / Chen, W. / Levin, A.M. / Connolly, J.M. / Zhu, C. / Kranz, D.M. / Garcia, K.C. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 500.1 KB | Display | ![]() |
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PDB format | ![]() | 412.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3tf7C ![]() 3tfkSC ![]() 3tjhC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 8 molecules BDHNIEKQ
#2: Protein | Mass: 27248.180 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pET28a / Production host: ![]() ![]() #3: Protein | Mass: 21072.260 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Antibody / Protein/peptide , 2 types, 8 molecules ACGMJFLR
#1: Antibody | Mass: 23326.877 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pET28a / Production host: ![]() ![]() #4: Protein/peptide | Mass: 1171.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: GenScript |
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-Non-polymers , 3 types, 20 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.4 Details: 1.1M lithium sulfate, 1% (v/v) PEG 200 and 0.1M sodium acetate pH 4.4, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 21, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→84.07 Å / Num. all: 104323 / Num. obs: 104323 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.9→3.06 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3TFK Resolution: 3.1→45.313 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 26.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.394 Å2 / ksol: 0.305 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.1→45.313 Å
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Refine LS restraints |
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LS refinement shell |
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