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Open data
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Basic information
Entry | Database: PDB / ID: 5hhp | ||||||
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Title | Crystal Structure of HLA-A*0201 in complex with M1-G4E | ||||||
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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 | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Gras, S. / Josephs, T.M. / Rossjohn, J. | ||||||
![]() | ![]() Title: Molecular basis for universal HLA-A*0201-restricted CD8+ T-cell immunity against influenza viruses. Authors: Valkenburg, S.A. / Josephs, T.M. / Clemens, E.B. / Grant, E.J. / Nguyen, T.H. / Wang, G.C. / Price, D.A. / Miller, A. / Tong, S.Y. / Thomas, P.G. / Doherty, P.C. / Rossjohn, J. / Gras, S. / Kedzierska, 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 | ![]() | 105.2 KB | Display | ![]() |
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PDB format | ![]() | 77.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5hhmC ![]() 5hhnC ![]() 5hhoC ![]() 5hhqC ![]() 3gsoS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 31753.139 Da / Num. of mol.: 1 / Fragment: UNP residues 25-298 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 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1038.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: GL biochem / Source: (synth.) synthetic construct (others) |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.22 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 18-22% PEG 3350, Na citrate pH 6.5, 0.1M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 18, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||
Reflection | Resolution: 1.9→48.95 Å / Num. all: 35010 / Num. obs: 35010 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 19.46 Å2 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.071 / Rrim(I) all: 0.196 / Net I/σ(I): 9.4 / Num. measured all: 265021 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3GSO Resolution: 1.9→46.267 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.89 / 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: 71.85 Å2 / Biso mean: 25.2125 Å2 / Biso min: 7.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→46.267 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %
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