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- PDB-3mgt: Crystal structure of a H5-specific CTL epitope variant derived fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mgt | ||||||
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Title | Crystal structure of a H5-specific CTL epitope variant derived from H5N1 influenza virus in complex with HLA-A*0201 | ||||||
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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 | ![]() ![]() | ||||||
![]() | Sun, Y. / Liu, J. / Yang, M. / Gao, F. / Zhou, J. / Kitamura, Y. | ||||||
![]() | ![]() Title: Identification and structural definition of H5-specific CTL epitopes restricted by HLA-A*0201 derived from the H5N1 subtype of influenza A viruses Authors: Sun, Y. / Liu, J. / Yang, M. / Gao, F. / Zhou, J. / Kitamura, Y. / Gao, B. / Tien, P. / Shu, Y. / Iwamoto, A. / Chen, Z. / Gao, G.F. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 342.7 KB | Display | ![]() |
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PDB format | ![]() | 277.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3mgoC ![]() 1jf1S 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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Unit cell |
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Components
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 4 / Fragment: Extracellular domain, UNP residues 25-275 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein | ![]() Mass: 11879.356 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Protein/peptide | Mass: 1241.412 Da / Num. of mol.: 4 / Fragment: Unp residues 205-214 / Source method: obtained synthetically Details: chemical synthesized; the sequence comes from the strain (A/Anhui/1/2005(H5N1). Source: (synth.) ![]() ![]() ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25mM MES(pH 6.5), 16% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 28, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.197→25.535 Å / Num. all: 76982 / Num. obs: 72653 / % possible obs: 95.8 % / Net I/σ(I): 23 / Num. measured all: 165362 |
Reflection shell | Resolution: 2.197→2.28 Å / Redundancy: 2.14 % / Mean I/σ(I) obs: 23 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1JF1 Resolution: 2.197→25.535 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 2 / Phase error: 25.76 / 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 / Bsol: 34.852 Å2 / ksol: 0.339 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.88 Å2 / Biso mean: 33.185 Å2 / Biso min: 14.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.197→25.535 Å
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Refine LS restraints |
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LS refinement shell |
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