+Open data
-Basic information
Entry | Database: PDB / ID: 6avg | ||||||
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Title | Crystal structure of the KFJ37 TCR-NY-ESO-1-HLA-B*07:02 complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Human Leukocyte Antigen / Major histocompatibility complex / Immunoglobulin / T cell receptor | ||||||
Function / homology | Function and homology information tRNA threonylcarbamoyladenosine metabolic process / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / T cell receptor complex / 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 ...tRNA threonylcarbamoyladenosine metabolic process / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / T cell receptor complex / 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 / secretory granule membrane / 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 / response to bacterium / 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 / defense response / 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 / sensory perception of smell / negative regulation of neuron projection development / 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 / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / cell surface receptor signaling pathway / 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 / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Gully, B.S. / Gras, S. / Rossjohn, J. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Divergent T-cell receptor recognition modes of a HLA-I restricted extended tumour-associated peptide. Authors: Chan, K.F. / Gully, B.S. / Gras, S. / Beringer, D.X. / Kjer-Nielsen, L. / Cebon, J. / McCluskey, J. / Chen, W. / Rossjohn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6avg.cif.gz | 351.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6avg.ent.gz | 287.4 KB | Display | PDB format |
PDBx/mmJSON format | 6avg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/6avg ftp://data.pdbj.org/pub/pdb/validation_reports/av/6avg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules HAGF
#1: Protein | Mass: 12519.033 Da / Num. of mol.: 2 / Fragment: UNP residues 13-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 #4: Protein | Mass: 40508.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli (E. coli) / References: UniProt: P01889 |
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-T-cell receptor ... , 2 types, 4 molecules CBDE
#2: Protein | Mass: 22532.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J268 #3: Protein | Mass: 27548.471 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV9 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J1U6 |
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-Protein/peptide / Non-polymers , 2 types, 506 molecules QP
#5: Protein/peptide | Mass: 1149.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P78358*PLUS #6: Water | ChemComp-HOH / | |
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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: 2.28 Å3/Da / Density % sol: 46.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 0.1 M BTP pH 8.8, 0.2 M Na-Iodide, 14 % w/v PEG 3350 and 2 % w/v PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→38.815 Å / Num. obs: 55986 / % possible obs: 98.8 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 8124 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→38.815 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→38.815 Å
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Refine LS restraints |
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LS refinement shell |
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