[English] 日本語
Yorodumi- PDB-1bd2: COMPLEX BETWEEN HUMAN T-CELL RECEPTOR B7, VIRAL PEPTIDE (TAX) AND... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bd2 | ||||||
---|---|---|---|---|---|---|---|
Title | COMPLEX BETWEEN HUMAN T-CELL RECEPTOR B7, VIRAL PEPTIDE (TAX) AND MHC CLASS I MOLECULE HLA-A 0201 | ||||||
Components |
| ||||||
Keywords | COMPLEX (MHC/VIRAL PEPTIDE/RECEPTOR) / COMPLEX (MHC-VIRAL PEPTIDE-RECEPTOR) / COMPLEX (MHC-VIRAL PEPTIDE-RECEPTOR) complex | ||||||
Function / homology | Function and homology information MHC protein binding / symbiont-mediated perturbation of host exit from mitosis / : / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 ...MHC protein binding / symbiont-mediated perturbation of host exit from mitosis / : / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / Generation of second messenger molecules / 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 / PD-1 signaling / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / regulation of immune response / 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 / regulation of mRNA stability / 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 / 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 / Downstream TCR signaling / 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 / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / adaptive immune response / learning or memory Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human T-lymphotropic virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Ding, Y.-H. / Smith, K.J. / Garboczi, D.N. / Utz, U. / Biddison, W.E. / Wiley, D.C. | ||||||
Citation | Journal: Immunity / Year: 1998 Title: Two human T cell receptors bind in a similar diagonal mode to the HLA-A2/Tax peptide complex using different TCR amino acids. Authors: Ding, Y.H. / Smith, K.J. / Garboczi, D.N. / Utz, U. / Biddison, W.E. / Wiley, D.C. #1: Journal: Nature / Year: 1996 Title: Structure of the Complex between Human T-Cell Receptor, Viral Peptide and Hla-A2 Authors: Garboczi, D.N. / Ghosh, P. / Utz, U. / Fan, Q.R. / Biddison, W.E. / Wiley, D.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bd2.cif.gz | 169.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bd2.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bd2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/1bd2 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/1bd2 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS ALPHA 1, ALPHA 2, ALPHA 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: PLASMA MEMBRANECell membrane / Gene: HLA-A 0201 / Organ: PLASMA / Plasmid: PHN1 Cellular location (production host): REFOLDED FROM INCLUSION BODIES Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P01892, UniProt: P04439*PLUS |
---|---|
#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: EXTRACELLULARGlossary of biology / Gene: V BETA 12.3 J BETA 2.7 (BV13S1) / Organ: PLASMA / Plasmid: PLM1 / Species (production host): Escherichia coli Cellular location (production host): REFOLDED FROM INCLUSION BODIES Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P61769 |
-T CELL RECEPTOR ... , 2 types, 2 molecules DE
#4: Protein | Mass: 22730.295 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS V AND C, RESIDUES 1 - 210 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: T-LYMPHOCYTE / Cell line: BL21 / Cellular location: PLASMA MEMBRANECell membrane / Gene: V ALPHA 17.2, J ALPHA 54 (ADV21S1A1N2) / Organ: PLASMA / Plasmid: PLM1 / Species (production host): Escherichia coli Cellular location (production host): REFOLDED FROM INCLUSION BODIES Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 338766, UniProt: P04437*PLUS |
---|---|
#5: Protein | Mass: 27326.229 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS V AND C, RESIDUES 1 - 247 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: T-LYMPHOCYTE / Cell line: BL21 / Cellular location: PLASMA MEMBRANECell membrane / Gene: V BETA 12.3, J BETA 2.7 (BV13S1) / Organ: PLASMA / Plasmid: PLM1 / Species (production host): Escherichia coli Cellular location (production host): REFOLDED FROM INCLUSION BODIES Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 3002925, UniProt: A0A0K0K1A5*PLUS |
-Protein/peptide / Non-polymers , 2 types, 40 molecules C
#3: Protein/peptide | Mass: 1070.280 Da / Num. of mol.: 1 Fragment: RESIDUES 11 - 19 FROM TAX PROTEIN OF HUMAN T LYMPHOTROPIC VIRUS TYPE 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human T-lymphotropic virus 1 / Genus: Deltaretrovirus / Species: Primate T-lymphotropic virus 1 / References: UniProt: P14079*PLUS |
---|---|
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 58 % |
---|---|
Crystal grow | pH: 7.1 Details: 12% PEG8000, 20MM MOPS, 100MM MAGNESIUM ACETATE,PH7.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Feb 5, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 33899 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 59.1 Å2 / Rmerge(I) obs: 0.11 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.22 / % possible all: 85.1 |
Reflection | *PLUS Num. measured all: 145021 |
Reflection shell | *PLUS % possible obs: 85.1 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1HHI AND 1AO7 Resolution: 2.5→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1000000 / Data cutoff low absF: 1.0E-5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|