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Yorodumi- PDB-5nht: human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptid... -
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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 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Melan-A/MART-1 PEPTIDE / DECAPEPTIDE / MHC CLASS I / HLA-A2 / T cell receptor | ||||||
Function / homology | Function and homology information T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation ...T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / trans-Golgi network / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / 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 / melanosome / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Exertier, C. / Reiser, J.-B. / Lantez, V. / Chouquet, A. / Bonneville, M. / Saulquin, X. / Housset, D. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nht.cif.gz | 181.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nht.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 5nht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/5nht ftp://data.pdbj.org/pub/pdb/validation_reports/nh/5nht | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / Variant (production host): X90F LAQQ1 / References: UniProt: P01892, UniProt: P04439*PLUS |
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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.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / Variant (production host): X90F LAQQ1 / References: UniProt: P61769 |
-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.) Homo sapiens (human) / References: UniProt: Q16655*PLUS |
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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.) Homo sapiens (human) / Gene: TRAV12-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: A0A075B6T6, UniProt: K7N5N2 |
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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.) Homo sapiens (human) / Gene: TCRBV17S1A1T, TRBV19, TRB / Plasmid: pJexpress414 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: A0A5B3, UniProt: A0A0C4ZKA8 |
-Non-polymers , 4 types, 5 molecules
#6: Chemical | ChemComp-SCN / | ||||
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#7: Chemical | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979742 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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