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Yorodumi- PDB-3vxu: The complex between T36-5 TCR and HLA-A24 bound to HIV-1 Nef134-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vxu | ||||||
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Title | The complex between T36-5 TCR and HLA-A24 bound to HIV-1 Nef134-10(2F) peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 / NEF / HLA-A24 / T CELL RECEPTOR / MHC CLASS I / IMMUNOGLOBURIN DOMAIN / TCR / MHC / IMMUNE RESPONSE | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / host cell Golgi membrane / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna ...symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / host cell Golgi membrane / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / 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 / T cell receptor binding / 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 / virion component / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / 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 / SH3 domain binding / 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 / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / 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 / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Shimizu, A. / Fukai, S. / Yamagata, A. / Iwamoto, A. | ||||||
Citation | Journal: SCI REP / Year: 2013 Title: Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection Authors: Shimizu, A. / Kawana-Tachikawa, A. / Yamagata, A. / Han, C. / Zhu, D. / Sato, Y. / Nakamura, H. / Koibuchi, T. / Carlson, J. / Martin, E. / Brumme, C.J. / Shi, Y. / Gao, G.F. / Brumme, Z.L. ...Authors: Shimizu, A. / Kawana-Tachikawa, A. / Yamagata, A. / Han, C. / Zhu, D. / Sato, Y. / Nakamura, H. / Koibuchi, T. / Carlson, J. / Martin, E. / Brumme, C.J. / Shi, Y. / Gao, G.F. / Brumme, Z.L. / Fukai, S. / Iwamoto, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vxu.cif.gz | 329.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vxu.ent.gz | 269.7 KB | Display | PDB format |
PDBx/mmJSON format | 3vxu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/3vxu ftp://data.pdbj.org/pub/pdb/validation_reports/vx/3vxu | HTTPS FTP |
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-Related structure data
Related structure data | 3vxmC 3vxnSC 3vxoC 3vxpC 3vxqC 3vxrC 3vxsC 3vxtSC 3w0wC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31683.086 Da / Num. of mol.: 2 / Fragment: UNP residues 25-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: PET21D(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P05534, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: PET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769 #3: Protein/peptide | Mass: 1274.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YYU3 #4: Protein | Mass: 22764.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 #5: Protein | Mass: 27577.764 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 |
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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: 3.39 Å3/Da / Density % sol: 63.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% PEG3350, 0.1M sodium nitrate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å | |||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 2, 2010 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.7→50 Å / Num. obs: 62839 / % possible obs: 92.2 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.078 / Net I/σ(I): 12.6 | |||||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.344 / Num. unique all: 5460 / % possible all: 80.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VXT, 3VXN Resolution: 2.7→32.35 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 5663552.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED. THIS STRUCTURE WAS REFINED AS A PERFECT TWIN.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: -6.37733 Å2 / ksol: 0.2 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→32.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree: 0.3868 / Rfactor Rwork: 0.4004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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