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Yorodumi- PDB-6rp9: Crystal structure of the T-cell receptor NYE_S3 bound to HLA A2*0... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rp9 | ||||||
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Title | Crystal structure of the T-cell receptor NYE_S3 bound to HLA A2*01-SLLMWITQV | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T-cell receptor / peptide-Human leukocyte antigen complex / NY-ESO-1 / cancer testis antigen | ||||||
Function / homology | Function and homology information tRNA threonylcarbamoyladenosine metabolic process / 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 ...tRNA threonylcarbamoyladenosine metabolic process / 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 / 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 / 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 / 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 / structural molecule activity / Golgi apparatus / cell surface Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å | ||||||
Authors | Coles, C.H. / Mulvaney, R. / Malla, S. / Lloyd, A. / Smith, K. / Chester, F. / Knox, A. / Stacey, A.R. / Dukes, J. / Baston, E. ...Coles, C.H. / Mulvaney, R. / Malla, S. / Lloyd, A. / Smith, K. / Chester, F. / Knox, A. / Stacey, A.R. / Dukes, J. / Baston, E. / Griffin, S. / Vuidepot, A. / Jakobsen, B.K. / Harper, S. | ||||||
Citation | Journal: J Immunol. / Year: 2020 Title: TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex. Authors: Coles, C.H. / Mulvaney, R.M. / Malla, S. / Walker, A. / Smith, K.J. / Lloyd, A. / Lowe, K.L. / McCully, M.L. / Martinez Hague, R. / Aleksic, M. / Harper, J. / Paston, S.J. / Donnellan, Z. / ...Authors: Coles, C.H. / Mulvaney, R.M. / Malla, S. / Walker, A. / Smith, K.J. / Lloyd, A. / Lowe, K.L. / McCully, M.L. / Martinez Hague, R. / Aleksic, M. / Harper, J. / Paston, S.J. / Donnellan, Z. / Chester, F. / Wiederhold, K. / Robinson, R.A. / Knox, A. / Stacey, A.R. / Dukes, J. / Baston, E. / Griffin, S. / Jakobsen, B.K. / Vuidepot, A. / Harper, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rp9.cif.gz | 843.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rp9.ent.gz | 711.5 KB | Display | PDB format |
PDBx/mmJSON format | 6rp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/6rp9 ftp://data.pdbj.org/pub/pdb/validation_reports/rp/6rp9 | HTTPS FTP |
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-Related structure data
Related structure data | 6rpaC 6rpbC 3qdjS 5d2nS 5e00S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 32082.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 #3: Protein/peptide | Mass: 1090.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P78358 #4: Protein | Mass: 22844.078 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #5: Protein | Mass: 27621.572 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulphate, 15 % PEG8k, 0.1 M Tris pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 3.12→85.61 Å / Num. obs: 52792 / % possible obs: 100 % / Redundancy: 6.76 % / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.047 / Net I/σ(I): 10.99 |
Reflection shell | Resolution: 3.12→3.2 Å / Redundancy: 3.97 % / Rmerge(I) obs: 0.999 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 2717 / CC1/2: 0.627 / Rpim(I) all: 0.567 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5e00 (chains A and B), 3QDJ (chain D) and 5D2N (chain E) Resolution: 3.12→68.01 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU B: 62.726 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 117.682 Å2
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Refinement step | Cycle: LAST / Resolution: 3.12→68.01 Å
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Refine LS restraints |
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