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Yorodumi- PDB-2oje: Mycoplasma arthritidis-derived mitogen complexed with class II MH... -
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-Basic information
Entry | Database: PDB / ID: 2oje | ||||||
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Title | Mycoplasma arthritidis-derived mitogen complexed with class II MHC molecule HLA-DR1/HA complex in the presence of EDTA | ||||||
Components |
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Keywords | IMMUNE SYSTEM / superantigen / MHC | ||||||
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 / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of T cell mediated immune response to tumor cell / 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 / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of T cell mediated immune response to tumor cell / 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 / CD4 receptor binding / positive regulation of monocyte differentiation / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / T-helper 1 type immune response / polysaccharide binding / transport vesicle membrane / 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 / macrophage differentiation / humoral immune response / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / epidermis development / PD-1 signaling / trans-Golgi network membrane / 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 / cognition / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / 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 / positive regulation of immune response / Interferon gamma signaling / endocytic vesicle membrane / 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 / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of viral entry into host cell / host cell surface receptor binding / immune response / positive regulation of protein phosphorylation / apical plasma membrane / lysosomal membrane / Golgi membrane / external side of plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å | ||||||
Authors | Li, H. / Zhao, Y. / Guo, Y. / Li, Z. / Eisele, L. / Mourad, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Zinc induces dimerization of the class II major histocompatibility complex molecule that leads to cooperative binding to a superantigen. Authors: Li, H. / Zhao, Y. / Guo, Y. / Li, Z. / Eisele, L. / Mourad, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oje.cif.gz | 254.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oje.ent.gz | 206 KB | Display | PDB format |
PDBx/mmJSON format | 2oje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oje_validation.pdf.gz | 494.1 KB | Display | wwPDB validaton report |
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Full document | 2oje_full_validation.pdf.gz | 535.8 KB | Display | |
Data in XML | 2oje_validation.xml.gz | 47.6 KB | Display | |
Data in CIF | 2oje_validation.cif.gz | 65.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/2oje ftp://data.pdbj.org/pub/pdb/validation_reports/oj/2oje | HTTPS FTP |
-Related structure data
Related structure data | 1r5iS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-HLA class II histocompatibility antigen, ... , 2 types, 4 molecules AEBF
#1: Protein | Mass: 21112.354 Da / Num. of mol.: 2 / Fragment: extracellular domain, residues 27-206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / 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: extracellular domain, residues 30-219 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P04229, UniProt: P01911*PLUS |
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-Protein/peptide / Protein , 2 types, 4 molecules CGDH
#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 / References: UniProt: Q91LS8*PLUS #4: Protein | Mass: 25419.404 Da / Num. of mol.: 2 / Fragment: residues 25-238 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 |
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-Non-polymers , 2 types, 122 molecules
#5: Chemical | ChemComp-PO4 / #6: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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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: 3.97 Å3/Da / Density % sol: 68.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 1.7M potassium sodium phosphate, 0.1M HEPES, 2 mM EDTA, pH 7.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2003 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3→40.22 Å / Num. obs: 40345 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.124 / Rsym value: 12.4 / Net I/σ(I): 17 |
Reflection shell | Resolution: 3→3.19 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6761 / Rsym value: 56.3 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1R5I Resolution: 3→40.22 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2671296.25 / 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: 18.6402 Å2 / ksol: 0.34148 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→40.22 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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