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- PDB-6g9q: Ternary complex of P14 TCR with murine MHC class I H-2 Db in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6g9q | ||||||
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Title | Ternary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen derived from dopamine monooxygenase. | ||||||
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![]() | IMMUNE SYSTEM / LCMV / cross-reactivity / MHC class I / TCR / APL | ||||||
Function / homology | ![]() regulation of vascular associated smooth muscle cell proliferation / Catecholamine biosynthesis / octopamine metabolic process / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / octopamine biosynthetic process / homoiothermy / regulation of vascular endothelial cell proliferation / chromaffin granule lumen ...regulation of vascular associated smooth muscle cell proliferation / Catecholamine biosynthesis / octopamine metabolic process / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / octopamine biosynthetic process / homoiothermy / regulation of vascular endothelial cell proliferation / chromaffin granule lumen / regulation of extrinsic apoptotic signaling pathway / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / norepinephrine biosynthetic process / Generation of second messenger molecules / varicosity / chromaffin granule membrane / Downstream TCR signaling / behavioral response to ethanol / dopamine catabolic process / maternal behavior / alpha-beta T cell receptor complex / fear response / vasoconstriction / L-ascorbic acid binding / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transport vesicle membrane / T cell receptor complex / response to pain / leukocyte migration / associative learning / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / centriolar satellite / blood vessel remodeling / beta-2-microglobulin binding / cellular defense response / positive regulation of vasoconstriction / immunoglobulin complex, circulating / immunoglobulin receptor binding / response to amphetamine / Neutrophil degranulation / secretory granule membrane / locomotory behavior / complement activation, classical pathway / 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 / antigen binding / peptide binding / response to bacterium / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / visual learning / regulation of erythrocyte differentiation / 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 / T cell mediated cytotoxicity / terminal bouton / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / memory / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / apical part of cell / negative regulation of neuron projection development / MHC class II protein complex binding / glucose homeostasis / late endosome membrane / positive regulation of cold-induced thermogenesis / iron ion transport / antibacterial humoral response / T cell differentiation in thymus / cytoplasmic vesicle / protein refolding / protein homotetramerization / secretory granule lumen Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Achour, A. / Sandalova, T. / Allerbring, E. | ||||||
![]() | ![]() Title: Structural basis for CD8+ T cells auto-reactivity in LCMV infection Authors: Allerbring, E. / Duru, A.D. / Nygren, P.A. / Sandalova, T. / Achour, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 346.2 KB | Display | ![]() |
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PDB format | ![]() | 278.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.2 KB | Display | ![]() |
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Full document | ![]() | 479.5 KB | Display | |
Data in XML | ![]() | 30.3 KB | Display | |
Data in CIF | ![]() | 43.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6g9rC ![]() 1s7uS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 4 types, 4 molecules ABGH
#1: Protein | Mass: 32087.703 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: 13794.978 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 23030.656 Da / Num. of mol.: 1 / Fragment: UNP residues 22-120,UNP residues 1-88 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 26663.633 Da / Num. of mol.: 1 / Fragment: UNP residues 11-122,UNP residues 1-127 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules P
#5: Protein/peptide | Mass: 1038.173 Da / Num. of mol.: 1 / Fragment: UNP residues 557-565 / Mutation: L3P / Source method: obtained synthetically / Details: Pro3 is replacement of Leu3 of wild type / Source: (synth.) ![]() ![]() |
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-Non-polymers , 2 types, 176 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
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#6: Chemical | ChemComp-GOL / |
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#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris HCl pH 8.0 PEG 6000 / PH range: 7.5-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50.5 Å / Num. obs: 80434 / % possible obs: 93.9 % / Redundancy: 3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.89→1.99 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8616 / % possible all: 69.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1S7U.pdb Resolution: 1.89→50.42 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.686 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.144 / 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: 42.842 Å2
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Refinement step | Cycle: 1 / Resolution: 1.89→50.42 Å
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