[English] 日本語
![](img/lk-miru.gif)
- 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 | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM/TOXIN / IMMUNE SYSTEM-TOXIN COMPLEX | ||||||
Function / homology | ![]() 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 / alpha-beta T cell receptor complex / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / transport vesicle membrane / intermediate filament / 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 / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / immunoglobulin complex, circulating / immunoglobulin receptor binding / MHC class II antigen presentation / viral budding from plasma membrane / trans-Golgi network membrane / complement activation, classical pathway / lumenal side of endoplasmic reticulum membrane / protein tetramerization / antigen binding / response to bacterium / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / toxin activity / early endosome membrane / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / membrane => GO:0016020 / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / blood microparticle / endosome membrane / host cell surface receptor binding / positive regulation of protein phosphorylation / immune response / 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 | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rodstrom, K.E.J. / Elbing, K. / Lindkvist-Petersson, K. | ||||||
![]() | ![]() 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: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 414.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 331.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 519.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 541.5 KB | Display | |
Data in XML | ![]() | 66.7 KB | Display | |
Data in CIF | ![]() | 91.4 KB | Display | |
Arichive directory | ![]() ![]() | 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.) ![]() ![]() ![]() #2: Protein | Mass: 27770.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-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.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 21155.904 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | Mass: 22080.664 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-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.) ![]() ![]() |
---|
-Non-polymers , 2 types, 27 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
---|
-
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: ![]() ![]() ![]() |
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: ![]() 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
|