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- PDB-5nqk: human 199.16 TCR in complex with Melan-A/MART-1 (26-35) peptide a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nqk | ||||||
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Title | human 199.16 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 | ![]() alpha-beta T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / T cell receptor complex / positive regulation of memory T cell activation / 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 ...alpha-beta T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / T cell receptor complex / positive regulation of memory T cell activation / 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 / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / alpha-beta T cell activation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Generation of second messenger molecules / TAP binding / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / 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 / DAP12 interactions / negative regulation of receptor binding / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / 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 / 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 / trans-Golgi network / 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 / 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 / specific granule lumen / recycling endosome membrane / 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 / 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 / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / melanosome / Downstream TCR signaling / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Exertier, C. / Reiser, J.-B. / Lantez, V. / Chouquet, A. / Bonneville, M. / Saulquin, X. / Housset, D. | ||||||
![]() | ![]() Title: human 199.16 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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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.7 KB | Display | ![]() |
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PDB format | ![]() | 141.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.4 KB | Display | ![]() |
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Full document | ![]() | 475.2 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 39.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nhtS 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
-Protein , 2 types, 2 molecules HL
#1: Protein | Mass: 31979.367 Da / Num. of mol.: 1 / 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-T-cell receptor ... , 2 types, 2 molecules AB
#4: Protein | Mass: 23090.320 Da / Num. of mol.: 1 / Mutation: T158C,T158C,T158C Source method: isolated from a genetically manipulated source Details: NUMBERING: RESIDUE 1 MATCH FIRST RESIDUE OF TRAV 12-2 DEFINED IN IMGT. ADDITIONAL SEQUENCE IN C-TER (ENDGGGCK) TO ENHANCE ALPHA-BETA CHAIN PAIRING. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A075B6T6, UniProt: A0A075B6X0, UniProt: A0A1B0GUM0, UniProt: P01848*PLUS |
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#5: Protein | Mass: 28292.430 Da / Num. of mol.: 1 / Mutation: S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C Source method: isolated from a genetically manipulated source Details: NUMBERING: RESIDUE 1 MATCH FIRST RESIDUE OF TRBV 19 DEFINED IN IMGT. ADDITIONAL SEQUENCE IN C-TER (DQDRGGGCD) TO ENHANCE ALPHA-BETA CHAIN PAIRING. Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A5B3, UniProt: A0A0C4ZKA8, UniProt: A0A075B6N1*PLUS |
-Protein/peptide / Non-polymers , 2 types, 2 molecules P![](data/chem/img/NA.gif)
![](data/chem/img/NA.gif)
#3: Protein/peptide | Mass: 985.176 Da / Num. of mol.: 1 / Mutation: A27L / Source method: obtained synthetically / Source: (synth.) ![]() |
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#6: Chemical | ChemComp-NA / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG3350 11%, bis-tris propane pH 6.5 0.1M, KNa tartrate 0.1M |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→48.53 Å / Num. obs: 16830 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rsym value: 0.173 / Net I/σ(I): 6.28 |
Reflection shell | Resolution: 3.25→3.33 Å / Redundancy: 3.43 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1236 / CC1/2: 0.523 / Rsym value: 1.611 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5NHT Resolution: 3.25→48.53 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.837 / SU B: 50.604 / SU ML: 0.742 / Cross valid method: THROUGHOUT / ESU R Free: 0.759 / 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: 109.51 Å2
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Refinement step | Cycle: 1 / Resolution: 3.25→48.53 Å
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