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Open data
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Basic information
Entry | Database: PDB / ID: 6jp3 | ||||||
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Title | Crystal structure of peptide in complex with HLA-A1101. | ||||||
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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 | ![]() ![]() ![]() | ||||||
![]() | Huan, X. / Xiao, Z. / Ren, E.C. | ||||||
![]() | ![]() Title: Crystal structure of suboptimal viral fragments of Epstein Barr Virus Rta peptide-HLA complex that stimulate CD8 T cell response. Authors: Huan, X. / Zhuo, Z. / Xiao, Z. / Ren, E.C. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.1 KB | Display | ![]() |
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PDB format | ![]() | 79.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6jozC ![]() 1x7qS 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 , 2 types, 2 molecules AB
#1: Protein | Mass: 31855.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Fragment: extracellular domain alpha 1, alpha 2 and alpha 3 Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
-Protein/peptide , 2 types, 2 molecules CD
#3: Protein/peptide | Mass: 461.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized peptide / Source: (synth.) synthetic construct (others) |
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#4: Protein/peptide | Mass: 512.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized peptide / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 451 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 60.01 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2M Sodium malonate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.66→64.27 Å / Num. obs: 64100 / % possible obs: 99 % / Redundancy: 7.2 % / CC1/2: 0.951 / Rrim(I) all: 0.07 / Net I/σ(I): 2.4 |
Reflection shell | Resolution: 1.66→1.703 Å / CC1/2: 0.824 / Rrim(I) all: 0.858 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1X7Q Resolution: 1.66→64.26 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.565 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.081 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.409 Å2
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Refinement step | Cycle: 1 / Resolution: 1.66→64.26 Å
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