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- PDB-5nht: human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nht | ||||||
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Title | human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2 | ||||||
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![]() | IMMUNE SYSTEM / Melan-A/MART-1 PEPTIDE / DECAPEPTIDE / MHC CLASS I / HLA-A2 / T cell receptor | ||||||
Function / homology | ![]() Regulation of MITF-M-dependent genes involved in pigmentation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / T cell receptor complex / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding ...Regulation of MITF-M-dependent genes involved in pigmentation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / T cell receptor complex / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / 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 / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / trans-Golgi network / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of type II interferon production / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / melanosome / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Exertier, C. / Reiser, J.-B. / Lantez, V. / Chouquet, A. / Bonneville, M. / Saulquin, X. / Housset, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2 Authors: Exertier, C. / Reiser, J.-B. / Housset, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 181.4 KB | Display | ![]() |
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PDB format | ![]() | 140.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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 HL
#1: Protein | Mass: 31979.367 Da / Num. of mol.: 1 / Fragment: UNP Residues 25-300 / Mutation: A245V 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 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules P
#3: Protein/peptide | Mass: 985.176 Da / Num. of mol.: 1 / Mutation: A27L / Source method: obtained synthetically / Source: (synth.) ![]() |
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-T-cell receptor ... , 2 types, 2 molecules AB
#4: Protein | Mass: 23132.400 Da / Num. of mol.: 1 / Mutation: T158C,T158C Source method: isolated from a genetically manipulated source Details: Numbering: residue 1 match first residue of TRAV12-2 defined in IMGT. Additional sequence in C-ter (ENDGGGCK) to enhance alpha-beta chain pairing. Source: (gene. exp.) ![]() ![]() ![]() |
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#5: Protein | Mass: 28292.430 Da / Num. of mol.: 1 Mutation: S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C Source method: isolated from a genetically manipulated source Details: Numbering: residue 1 match first residue of TRBV19 defined in IMGT. Additional sequence in C-ter (DQDRGGGCD) to enhance alpha-beta chain pairing. Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 5 molecules ![](data/chem/img/SCN.gif)
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#6: Chemical | ChemComp-SCN / | ||||
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#7: Chemical | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG3350 8 %, K Thiocyanate 0.1 M, Bis-Tris propane pH 6.5 0.1 M, protein concentration 3.5 mg/ml |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2015 / Details: Si with Pt coating |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979742 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→16 Å / Num. obs: 17189 / % possible obs: 98.5 % / Redundancy: 3.66 % / Biso Wilson estimate: 62.12 Å2 / CC1/2: 0.99 / Rsym value: 0.142 / Net I/σ(I): 4.79 |
Reflection shell | Resolution: 3.2→3.29 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.26 / Num. unique obs: 1282 / CC1/2: 0.86 / Rsym value: 0.561 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OGA, 3QDJ Resolution: 3.2→16 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.826 / SU B: 35.758 / SU ML: 0.59 / Cross valid method: THROUGHOUT / ESU R Free: 0.671 / 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: 72.846 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→16 Å
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