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Yorodumi- PDB-1j8h: Crystal Structure of a Complex of a Human alpha/beta-T cell Recep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j8h | |||||||||
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Title | Crystal Structure of a Complex of a Human alpha/beta-T cell Receptor, Influenza HA Antigen Peptide, and MHC Class II Molecule, HLA-DR4 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / protein-protein complex / immunoglobulin fold | |||||||||
Function / homology | Function and homology information regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / alpha-beta T cell receptor complex / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / intermediate filament / transport vesicle membrane / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / alpha-beta T cell activation / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / viral budding from plasma membrane / trans-Golgi network membrane / clathrin-coated endocytic vesicle membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / response to bacterium / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / lysosome / host cell surface receptor binding / positive regulation of protein phosphorylation / immune response / Golgi membrane / external side of plasma membrane / fusion of virus membrane with host plasma membrane / lysosomal membrane / fusion of virus membrane with host endosome membrane / viral envelope / positive regulation of DNA-templated transcription / virion attachment to host cell / host cell plasma membrane / virion membrane / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Influenzavirus A | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Hennecke, J. / Wiley, D.C. | |||||||||
Citation | Journal: J.Exp.Med. / Year: 2002 Title: Structure of a complex of the human alpha/beta T cell receptor (TCR) HA1.7, influenza hemagglutinin peptide, and major histocompatibility complex class II molecule, HLA-DR4 (DRA*0101 and ...Title: Structure of a complex of the human alpha/beta T cell receptor (TCR) HA1.7, influenza hemagglutinin peptide, and major histocompatibility complex class II molecule, HLA-DR4 (DRA*0101 and DRB1*0401): insight into TCR cross-restriction and alloreactivity. Authors: Hennecke, J. / Wiley, D.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j8h.cif.gz | 186.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j8h.ent.gz | 144.6 KB | Display | PDB format |
PDBx/mmJSON format | 1j8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j8h_validation.pdf.gz | 784.3 KB | Display | wwPDB validaton report |
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Full document | 1j8h_full_validation.pdf.gz | 804.5 KB | Display | |
Data in XML | 1j8h_validation.xml.gz | 36 KB | Display | |
Data in CIF | 1j8h_validation.cif.gz | 50.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/1j8h ftp://data.pdbj.org/pub/pdb/validation_reports/j8/1j8h | HTTPS FTP |
-Related structure data
Related structure data | 1fytS 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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Unit cell |
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-Components
-HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 21084.826 Da / Num. of mol.: 1 / Fragment: Extracellular Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Schneider / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01903 |
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#2: Protein | Mass: 22505.994 Da / Num. of mol.: 1 / Fragment: Extracellular Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Schneider / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P13760, UniProt: P01911*PLUS |
-T-CELL RECEPTOR ... , 2 types, 2 molecules DE
#4: Protein | Mass: 23408.016 Da / Num. of mol.: 1 / Fragment: Extracellular Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: PIR: RWHUAC, UniProt: P01848*PLUS |
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#5: Protein | Mass: 28042.406 Da / Num. of mol.: 1 / Fragment: Extracellular Domain / Mutation: C192S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: PIR: S18894, UniProt: P01850*PLUS |
-Protein/peptide / Non-polymers , 2 types, 306 molecules C
#3: Protein/peptide | Mass: 1506.807 Da / Num. of mol.: 1 / Fragment: Antigen Peptide Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenzavirus A / Genus: Influenzavirus A / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03437 |
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#8: Water | ChemComp-HOH / |
-Sugars , 2 types, 3 molecules
#6: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#7: Sugar |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.35 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 13% PEG 8000, 1 M NaCl, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 11, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.81 Å / Num. all: 47712 / Num. obs: 46185 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 54.1 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.33 / % possible all: 96.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 46705 |
Reflection shell | *PLUS % possible obs: 96.37 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FYT.pdb Resolution: 2.4→19.81 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1769191.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.44 Å2 / ksol: 0.3465 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.208 / Rfactor Rfree: 0.245 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.358 / Rfactor Rwork: 0.32 |