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Open data
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Basic information
Entry | Database: PDB / ID: 5c0d | ||||||
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Title | HLA-A02 carrying AQWGPDPAAA | ||||||
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Function / homology | ![]() T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / TAP complex binding / negative regulation of fatty acid metabolic process / Golgi medial cisterna / negative regulation of feeding behavior / positive regulation of CD8-positive, alpha-beta T cell activation ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / TAP complex binding / negative regulation of fatty acid metabolic process / Golgi medial cisterna / negative regulation of feeding behavior / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Signaling by Insulin receptor / nitric oxide-cGMP-mediated signaling / IRS activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Insulin processing / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Rizkallah, P.J. / Bulek, A.M. / Cole, D.K. / Sewell, A.K. | ||||||
![]() | ![]() Title: Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity. Authors: Cole, D.K. / Bulek, A.M. / Dolton, G. / Schauenberg, A.J. / Szomolay, B. / Rittase, W. / Trimby, A. / Jothikumar, P. / Fuller, A. / Skowera, A. / Rossjohn, J. / Zhu, C. / Miles, J.J. / ...Authors: Cole, D.K. / Bulek, A.M. / Dolton, G. / Schauenberg, A.J. / Szomolay, B. / Rittase, W. / Trimby, A. / Jothikumar, P. / Fuller, A. / Skowera, A. / Rossjohn, J. / Zhu, C. / Miles, J.J. / Peakman, M. / Wooldridge, L. / Rizkallah, P.J. / 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 | ![]() | 186.3 KB | Display | ![]() |
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PDB format | ![]() | 146.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5c07C ![]() 5c08C ![]() 5c09C ![]() 5c0aC ![]() 5c0bC ![]() 5c0cC ![]() 5c0eC ![]() 5c0fC ![]() 5c0gC ![]() 5c0iC ![]() 5c0jC ![]() 5n1yC ![]() 3utqS ![]() 5c06 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: 31951.316 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300 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: 983.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.54 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M sodium malonate, 0.1M BIS TRIS propane, pH 6.5, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.68→31.221 Å / Num. all: 49373 / Num. obs: 49373 / % possible obs: 98.8 % / Redundancy: 3.9 % / Rpim(I) all: 0.056 / Rrim(I) all: 0.112 / Rsym value: 0.084 / Net I/av σ(I): 7.595 / Net I/σ(I): 8.7 / Num. measured all: 192943 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 0.35 / Cor.coef. Fo:Fc: 0.68 / Cor.coef. Io to Ic: 0.617
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3UTQ Resolution: 1.68→31.22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2081 / WRfactor Rwork: 0.165 / FOM work R set: 0.8332 / SU B: 5.179 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1013 / SU Rfree: 0.1043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.42 Å2 / Biso mean: 20.449 Å2 / Biso min: 7.88 Å2
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Refinement step | Cycle: final / Resolution: 1.68→31.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.724 Å / 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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