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- PDB-6uz1: Noncanonical binding of single-chain A6 TCR variant S3-4 in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6uz1 | ||||||
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Title | Noncanonical binding of single-chain A6 TCR variant S3-4 in complex with Tax/HLA-A2 | ||||||
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![]() | IMMUNE SYSTEM / single-chain T cell receptor / peptide Major Histocompatibility complex | ||||||
Function / homology | ![]() symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / regulation of mRNA stability / 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 ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / regulation of mRNA stability / 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 / SH3 domain binding / 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 / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / cellular response to lipopolysaccharide / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / negative regulation of gene expression / focal adhesion / signaling receptor binding / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / positive regulation of DNA-templated transcription / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ma, J. / Singh, N.K. | ||||||
![]() | ![]() Title: An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding Modes. Authors: Singh, N.K. / Alonso, J.A. / Harris, D.T. / Anderson, S.D. / Ma, J. / Hellman, L.M. / Rosenberg, A.M. / Kolawole, E.M. / Evavold, B.D. / Kranz, D.M. / Baker, B.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 603 KB | Display | ![]() |
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PDB format | ![]() | 423.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 270.3 KB | Display | ![]() |
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Full document | ![]() | 271.1 KB | Display | |
Data in XML | ![]() | 1.7 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ftvS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | An assembly that is closer to the conventional one may be generated by using chains A, B and C of the primary asymmetric unit, along with chains E and D generated by SymOp 1_554; or by using chains F, G and H of the primary asymmetric unit, along with chains I and J generated by SymOp 1_556 |
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Components
-Protein , 2 types, 4 molecules AFBG
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein/peptide , 1 types, 2 molecules CH
#3: Protein/peptide | Mass: 1070.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-T cell receptor, ... , 2 types, 4 molecules IDJE
#4: Protein | Mass: 11995.190 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | Mass: 12547.098 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 2 types, 10 molecules ![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 66.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10%w/v Polyethylene glycol 20,000, 100mMMES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jul 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 37072 / % possible obs: 99.4 % / Redundancy: 11 % / Biso Wilson estimate: 81.4 Å2 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.087 / Rrim(I) all: 0.289 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.978 / Num. unique obs: 1889 / CC1/2: 0.803 / Rpim(I) all: 0.648 / Rrim(I) all: 2.082 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FTV Resolution: 3.14→44.72 Å / SU ML: 0.4445 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4977
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 103.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.14→44.72 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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