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Open data
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Basic information
Entry | Database: PDB / ID: 6eqa | ||||||
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Title | HLA class I histocompatibility antigen | ||||||
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Function / homology | ![]() T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Rizkallah, P.J. / Cole, D.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: TCR-induced alteration of primary MHC peptide anchor residue. Authors: Madura, F. / Rizkallah, P.J. / Legut, M. / Holland, C.J. / Fuller, A. / Bulek, A. / Schauenburg, A.J. / Trimby, A. / Hopkins, J.R. / Wells, S.A. / Godkin, A. / Miles, J.J. / Sami, M. / Li, Y. ...Authors: Madura, F. / Rizkallah, P.J. / Legut, M. / Holland, C.J. / Fuller, A. / Bulek, A. / Schauenburg, A.J. / Trimby, A. / Hopkins, J.R. / Wells, S.A. / Godkin, A. / Miles, J.J. / Sami, M. / Li, Y. / Liddy, N. / Jakobsen, B.K. / Loveridge, E.J. / Cole, D.K. / Sewell, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 347.3 KB | Display | ![]() |
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PDB format | ![]() | 282.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6eqbC ![]() 3hg1S 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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Unit cell |
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Components
-Protein , 4 types, 4 molecules ABDE
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 21371.404 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#5: Protein | Mass: 27264.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 813.982 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 2 types, 5 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-SO4 / ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.54 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 25% PEG 4000 and 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 9, 2011 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||
Reflection | Resolution: 3.16→82.32 Å / Num. obs: 20733 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 13.4 | |||||||||||||||
Reflection shell |
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 31.83 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3HG1 Resolution: 3.16→68.13 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.872 / SU B: 46.161 / SU ML: 0.371 / SU R Cruickshank DPI: 0.3913 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.491 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 160 Å2 / Biso mean: 58.181 Å2 / Biso min: 25.58 Å2
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Refinement step | Cycle: final / Resolution: 3.16→68.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.159→3.241 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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