[English] 日本語
Yorodumi- PDB-4c56: X-ray structure of the complex between staphylococcal enterotoxin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c56 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the complex between staphylococcal enterotoxin B, T cell receptor and major histocompatibility complex class II | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM/TOXIN / IMMUNE SYSTEM-TOXIN COMPLEX | ||||||
Function / homology | Function and homology information regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / 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 / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / 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 / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / 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 / alpha-beta T cell activation / Generation of second messenger molecules / immunological synapse / : / PD-1 signaling / epidermis development / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / viral budding from plasma membrane / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / response to bacterium / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / 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 / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / toxin activity / T cell receptor signaling pathway / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / lysosome / membrane => GO:0016020 / positive regulation of ERK1 and ERK2 cascade / endosome membrane / host cell surface receptor binding / immune response / positive regulation of protein phosphorylation / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / Golgi membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) STAPHYLOCOCCUS AUREUS (bacteria) INFLUENZA A VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Rodstrom, K.E.J. / Elbing, K. / Lindkvist-Petersson, K. | ||||||
Citation | Journal: J.Immunol. / Year: 2014 Title: Structure of the Superantigen Staphylococcal Enterotoxin B in Complex with Tcr and Peptide-Mhc Demonstrates Absence of Tcr-Peptide Contacts. Authors: Rodstrom, K.E.J. / Elbing, K. / Lindkvist-Petersson, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4c56.cif.gz | 414.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4c56.ent.gz | 331.3 KB | Display | PDB format |
PDBx/mmJSON format | 4c56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/4c56 ftp://data.pdbj.org/pub/pdb/validation_reports/c5/4c56 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-T CELL RECEPTOR ... , 2 types, 4 molecules AGBH
#1: Protein | Mass: 22812.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P01848*PLUS #2: Protein | Mass: 27770.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-LYMPHOCYTE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A0A5B9*PLUS |
---|
-Protein , 3 types, 6 molecules CIDJEK
#3: Protein | Mass: 28281.953 Da / Num. of mol.: 2 / Fragment: OB-DOMAIN AND BETA-GRASP DOMAIN, RESIDUES 13-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K12 / Variant (production host): UL635 / References: UniProt: Q5MAA8, UniProt: P01552*PLUS #4: Protein | Mass: 21155.904 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P01903 #5: Protein | Mass: 22080.664 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: A9JJF6, UniProt: P01911*PLUS |
---|
-Protein/peptide , 1 types, 2 molecules FL
#6: Protein/peptide | Mass: 1506.807 Da / Num. of mol.: 2 / Fragment: HA PEPTIDE, RESIDUES 327-339 / Source method: obtained synthetically / Source: (synth.) INFLUENZA A VIRUS / References: UniProt: Q03909, UniProt: P03437*PLUS |
---|
-Non-polymers , 2 types, 27 molecules
#7: Chemical | ChemComp-GOL / |
---|---|
#8: Water | ChemComp-HOH / |
-Details
Sequence details | IMGT ACCESSION NUMBERS FOR CHAINS A,G TRAV22 01 01 (AE000660), TRAJ40 01 (M35620) AND TRAC 01 ...IMGT ACCESSION NUMBERS FOR CHAINS A,G TRAV22 01 01 (AE000660), TRAJ40 01 (M35620) AND TRAC 01 (X02883). PRODUCT OF SOMATIC RECOMBINAT |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE |
---|---|
Crystal grow | pH: 5.5 Details: 8% PEG 20000, 0.1 M SODIUM CITRATE PH 5.5, 0.09 M MAGNESIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07227 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2011 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07227 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→48.7 Å / Num. obs: 61924 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 82.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1OGA CHAINS D AND E, 2IAL CHAIN A, 1SEB CHAINS A, B AND C Resolution: 2.9→29.23 Å / Cor.coef. Fo:Fc: 0.8907 / Cor.coef. Fo:Fc free: 0.8727 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 3.964 / SU Rfree Blow DPI: 0.357
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.03 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.494 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→29.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→2.98 Å / Total num. of bins used: 20
|