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- PDB-7dzm: Crystal Structure of the cross-restricted T18A TCR and HLAB8101 b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dzm | |||||||||
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Title | Crystal Structure of the cross-restricted T18A TCR and HLAB8101 bound to HIV-1 Gag TL9 peptide | |||||||||
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![]() | IMMUNE SYSTEM / TCR and p-MHC complex / HIV epitope TL9 | |||||||||
Function / homology | ![]() antigen processing and presentation / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway ...antigen processing and presentation / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HIV-1 retropepsin / 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 / retroviral ribonuclease H / exoribonuclease H / 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 / exoribonuclease H activity / 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 / host multivesicular body / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / DNA integration / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / viral genome integration into host DNA / positive regulation of T cell mediated cytotoxicity / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / specific granule lumen / recycling endosome membrane / RNA stem-loop binding / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / RNA-directed DNA polymerase activity / Modulation by Mtb of host immune system / host cell / RNA-DNA hybrid ribonuclease activity / sensory perception of smell / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / ER-Phagosome pathway / iron ion transport / symbiont-mediated suppression of host gene expression / early endosome membrane / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / DNA recombination / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / learning or memory / DNA-directed DNA polymerase activity / symbiont entry into host cell / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / lipid binding / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / endoplasmic reticulum Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liu, Y. / Yin, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cross-reactive TCR with alloreactivity for immunodominant HIV-1 epitope Gag TL9 with enhanced control of viral infection Authors: Liu, Y. / San, D. / Yin, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 430.4 KB | Display | ![]() |
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PDB format | ![]() | 293.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.9 KB | Display | ![]() |
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Full document | ![]() | 464.6 KB | Display | |
Data in XML | ![]() | 34.4 KB | Display | |
Data in CIF | ![]() | 49.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dznC ![]() 4gg6S ![]() 4u1iS ![]() 4udtS 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 , 4 types, 4 molecules ABDE
#1: Protein | Mass: 32071.203 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.) ![]() ![]() ![]() |
#4: Protein | Mass: 27263.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 23008.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide / Non-polymers , 2 types, 424 molecules C![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#3: Protein/peptide | Mass: 1032.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.88 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Potassium chloride, 0.05 M HEPES pH 7.5, 35% v/v Pentaerythritol propoxylate (5/4 PO/OH) |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→46.55 Å / Num. obs: 56526 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 38.63 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03414 / Rrim(I) all: 0.04828 / Net I/σ(I): 15.84 |
Reflection shell | Resolution: 2.242→2.322 Å / Rmerge(I) obs: 0.3732 / Num. unique obs: 5547 / CC1/2: 0.865 / CC star: 0.963 / Rrim(I) all: 0.5277 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4u1i, 4GG6, 4UDT Resolution: 2.25→46.55 Å / SU ML: 0.3044 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6803 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→46.55 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 44.5675649105 Å / Origin y: 97.3127616472 Å / Origin z: 4.73058954554 Å
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Refinement TLS group | Selection details: all |