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Yorodumi- PDB-2icw: Crystal structure of a complete ternary complex between TCR, supe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2icw | ||||||
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Title | Crystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule | ||||||
Components |
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Keywords | IMMUNE SYSTEM / TCR / MHC / superantigen / protein-protein complex | ||||||
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 / 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 / T cell receptor complex / 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 / 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 / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / 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 / 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 / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / cell surface receptor signaling pathway / lysosome / immune response / positive regulation of protein phosphorylation / external side of plasma membrane / Golgi membrane / lysosomal membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mycoplasma arthritidis (bacteria) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å | ||||||
Authors | Wang, L. / Zhao, Y. / Li, H. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: Crystal structure of a complete ternary complex of TCR, superantigen and peptide-MHC. Authors: Wang, L. / Zhao, Y. / Li, Z. / Guo, Y. / Jones, L.L. / Kranz, D.M. / Mourad, W. / Li, H. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of chains J and L are consistent with the sequence of chain B in the PDB entry 1TCR |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2icw.cif.gz | 340.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2icw.ent.gz | 274.5 KB | Display | PDB format |
PDBx/mmJSON format | 2icw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/2icw ftp://data.pdbj.org/pub/pdb/validation_reports/ic/2icw | 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
-HLA class II histocompatibility antigen, ... , 2 types, 4 molecules ADBE
#1: Protein | Mass: 20983.176 Da / Num. of mol.: 2 / Fragment: residues 28-206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01903 #2: Protein | Mass: 22080.664 Da / Num. of mol.: 2 / Fragment: residues 30-219 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P04229, UniProt: P01911*PLUS |
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-T-cell receptor ... , 2 types, 4 molecules IKJL
#5: Protein | Mass: 12113.593 Da / Num. of mol.: 2 / Fragment: residues 21-131 / Mutation: W82R, L43P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01738 #6: Protein | Mass: 12184.312 Da / Num. of mol.: 2 / Mutation: G17E, G42E, L80S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04213, UniProt: A2NTY6*PLUS |
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-Protein/peptide / Protein / Non-polymers , 3 types, 309 molecules CFGH
#3: Protein/peptide | Mass: 1506.807 Da / Num. of mol.: 2 / Fragment: residues 306-318 / Source method: obtained synthetically / Details: This sequence occurs naturally in Influenza virus #4: Protein | Mass: 25332.328 Da / Num. of mol.: 2 / Fragment: residues 26-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma arthritidis (bacteria) / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q48898 #7: 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: 2.91 Å3/Da / Density % sol: 57.8 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 5.6 Details: 13-15% PEG 4000, 5% isopropanol, 0.1 M sodium citrate, 2 mM zinc acetate, pH 5.6, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97951 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 12, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.8 Å / Num. all: 78311 / Num. obs: 78311 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.7 / Num. unique all: 7476 / Rsym value: 0.58 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1R5I, 1TCR Resolution: 2.41→47.79 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2277677.75 / 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: 45.051 Å2 / ksol: 0.333 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.41→47.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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