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Open data
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Basic information
Entry | Database: PDB / ID: 8d5q | ||||||
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Title | TCR TG6 in complex with Ld-HF10 | ||||||
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![]() | IMMUNE SYSTEM / MHCI / CD8 T cell | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Wang, Y. / Dai, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Peptide Centric V beta Specific Germline Contacts Shape a Specialist T Cell Response. Authors: Wang, Y. / Tsitsiklis, A. / Devoe, S. / Gao, W. / Chu, H.H. / Zhang, Y. / Li, W. / Wong, W.K. / Deane, C.M. / Neau, D. / Slansky, J.E. / Thomas, P.G. / Robey, E.A. / Dai, S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 259 KB | Display | ![]() |
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PDB format | ![]() | 202.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.6 KB | Display | ![]() |
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Full document | ![]() | 495.2 KB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d5nC ![]() 8d5pC ![]() 1ld9S ![]() 3to4S ![]() 6x2t ![]() 6x30 S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 23161.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 27929.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 21101.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules E
#4: Protein/peptide | Mass: 1149.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 3 types, 211 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-MES / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 11 % w/v PEG 8000, 0.1 M MES 6.0, 0.24 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→90 Å / Num. obs: 29168 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rpim(I) all: 0.03 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 2.5→2.54 Å / Num. unique obs: 2864 / Rpim(I) all: 0.29 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LD9, 3TO4 Resolution: 2.501→45.022 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 15.549 / SU ML: 0.18 / Cross valid method: NONE / ESU R: 0.397 / ESU R Free: 0.248 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.211 Å2
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Refinement step | Cycle: LAST / Resolution: 2.501→45.022 Å
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Refine LS restraints |
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LS refinement shell |
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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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