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- PDB-6rpa: Crystal structure of the T-cell receptor NYE_S2 bound to HLA A2*0... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rpa | ||||||
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Title | Crystal structure of the T-cell receptor NYE_S2 bound to HLA A2*01-SLLMWITQV | ||||||
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![]() | IMMUNE SYSTEM / T-cell receptor / peptide-Human leukocyte antigen complex / NY-ESO-1 / cancer testis antigen | ||||||
Function / homology | ![]() tRNA threonylcarbamoyladenosine metabolic process / T cell mediated cytotoxicity directed against tumor cell target / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I ...tRNA threonylcarbamoyladenosine metabolic process / T cell mediated cytotoxicity directed against tumor cell target / 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 / 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 / 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 / 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 / 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 / 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 / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.2 KB | Display | ![]() |
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PDB format | ![]() | 133.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.6 KB | Display | ![]() |
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Full document | ![]() | 458.3 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 37.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rp9C ![]() 6rpbC ![]() 3revS ![]() 4dzbS ![]() 5e00S S: Starting model for refinement C: citing same article ( |
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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 AB
#1: Protein | Mass: 32082.512 Da / Num. of mol.: 1 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 DE
#4: Protein | Mass: 23422.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#5: Protein | Mass: 27392.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide / Non-polymers , 2 types, 50 molecules C![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#3: Protein/peptide | Mass: 1090.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.02 M sodium/potassium phosphate, 20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.56→66.51 Å / Num. obs: 37679 / % possible obs: 99.3 % / Redundancy: 7.66 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.025 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.56→2.6 Å / Redundancy: 7.94 % / Rmerge(I) obs: 2.07 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 1945 / CC1/2: 0.637 / Rpim(I) all: 0.775 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B) Resolution: 2.56→66.51 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 20.147 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.314 / 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: 80.735 Å2
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Refinement step | Cycle: LAST / Resolution: 2.56→66.51 Å
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Refine LS restraints |
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