[English] 日本語
Yorodumi- PDB-1jws: Crystal Structure of the Complex of the MHC Class II Molecule HLA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jws | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Complex of the MHC Class II Molecule HLA-DR1 (HA peptide 306-318) with the Superantigen SEC3 Variant 3B1 | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / HLA-DR1 alpha subunit / HLA-DR1 beta subunit / Mutation | ||||||
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 / 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 / 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 / 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 / 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 / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of protein phosphorylation / immune response / lysosomal membrane / external side of plasma membrane / Golgi 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Sundberg, E.J. / Andersen, P.S. / Schlievert, P.M. / Karjalainen, K. / Mariuzza, R.A. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structural, energetic, and functional analysis of a protein-protein interface at distinct stages of affinity maturation Authors: Sundberg, E.J. / Andersen, P.S. / Schlievert, P.M. / Karjalainen, K. / Mariuzza, R.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jws.cif.gz | 135.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jws.ent.gz | 110.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jws_validation.pdf.gz | 452.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jws_full_validation.pdf.gz | 471.3 KB | Display | |
Data in XML | 1jws_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 1jws_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/1jws ftp://data.pdbj.org/pub/pdb/validation_reports/jw/1jws | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21155.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01903 |
---|---|
#2: Protein | Mass: 22080.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04229, UniProt: P01911*PLUS |
#3: Protein/peptide | Mass: 1506.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The Peptide was Chemically Synthesized |
#4: Protein | Mass: 27659.986 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0L5 |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.66 Å3/Da / Density % sol: 73.6 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, Sodium Acetate, Ethylene Glycol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.008 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 40189 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.071 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.0495 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 228880 / Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / % possible obs: 100 % / Rmerge(I) obs: 0.495 |
-Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→14.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 265913.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| |||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.1915 Å2 / ksol: 0.328914 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 45.5 Å2
| |||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→14.99 Å
| |||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| |||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / % reflection Rfree: 4.2 % | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 2.69 Å |