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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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![]() | IMMUNE SYSTEM / IMMUNO / HLA-A02 / 1E6-TCR / Cross-reactivity | ||||||
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 / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of nitric oxide mediated signal transduction / Golgi medial cisterna ...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 / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of nitric oxide mediated signal transduction / Golgi medial cisterna / negative regulation of fatty acid metabolic process / positive regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of feeding behavior / Signaling by Insulin receptor / CD8 receptor binding / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / alpha-beta T cell activation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / negative regulation of respiratory burst involved in inflammatory response / TAP binding / positive regulation of dendritic spine maintenance / protection from natural killer cell mediated cytotoxicity / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / beta-2-microglobulin binding / negative regulation of lipid catabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / T cell receptor binding / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / detection of bacterium / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / positive regulation of nitric-oxide synthase activity / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / endosome lumen / 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 / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / positive regulation of cell differentiation / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / cellular response to iron(III) ion / wound healing / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / insulin receptor binding / regulation of synaptic plasticity / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / negative regulation of protein catabolic process / hormone activity 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
Summary document | ![]() | 438.9 KB | Display | ![]() |
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Full document | ![]() | 444.2 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: _
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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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