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Yorodumi- PDB-6uk4: Complex of T cell Receptor with HHAT Neoantigen Peptide KQWLVWLFL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uk4 | ||||||
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Title | Complex of T cell Receptor with HHAT Neoantigen Peptide KQWLVWLFL Presented by HLA-A206 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Neoantigen / Peptide/MHC / T cell receptor | ||||||
Function / homology | Function and homology information N-terminal peptidyl-L-cysteine N-palmitoylation / O-acyltransferase activity / HHAT G278V doesn't palmitoylate Hh-Np / palmitoyltransferase activity / smoothened signaling pathway / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen ...N-terminal peptidyl-L-cysteine N-palmitoylation / O-acyltransferase activity / HHAT G278V doesn't palmitoylate Hh-Np / palmitoyltransferase activity / smoothened signaling pathway / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Hedgehog ligand biogenesis / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / 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 / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Devlin, J.R. / Baker, B.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2020 Title: Structural dissimilarity from self drives neoepitope escape from immune tolerance. Authors: Devlin, J.R. / Alonso, J.A. / Ayres, C.M. / Keller, G.L.J. / Bobisse, S. / Vander Kooi, C.W. / Coukos, G. / Gfeller, D. / Harari, A. / Baker, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uk4.cif.gz | 391.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uk4.ent.gz | 287.3 KB | Display | PDB format |
PDBx/mmJSON format | 6uk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/6uk4 ftp://data.pdbj.org/pub/pdb/validation_reports/uk/6uk4 | HTTPS FTP |
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-Related structure data
Related structure data | 6ujoC 6ujqC 6uk2C 1tvhS 5c0bS 5jziS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32001.398 Da / Num. of mol.: 1 / Fragment: UNP residues 25-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue / References: UniProt: U5YJP1 |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 Blue / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1233.521 Da / Num. of mol.: 1 / Fragment: Neoantigen peptide (UNP residues 68-76) / Mutation: L75F / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q5VTY9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
#4: Protein | Mass: 23541.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 DE3 |
#5: Protein | Mass: 27783.045 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 DE3 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.1 M sodium citrate, pH 6.3, 7.5% PEG6000, 0.2 M lithium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2019 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→50 Å / Num. obs: 35931 / % possible obs: 99 % / Redundancy: 7.8 % / Biso Wilson estimate: 63.92 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.042 / Rrim(I) all: 0.121 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.69→2.74 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1672 / CC1/2: 0.908 / Rpim(I) all: 0.195 / Rrim(I) all: 0.539 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1TVH, 5JZI, & 5C0B Resolution: 2.7→49.47 Å / SU ML: 0.3996 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9451
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→49.47 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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