[English] 日本語
Yorodumi- PDB-1n3n: Crystal structure of a mycobacterial hsp60 epitope with the murin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n3n | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a mycobacterial hsp60 epitope with the murine class I MHC molecule H-2Db | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin fold | ||||||
Function / homology | Function and homology information TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ciatto, C. / Capitani, G. / Tissot, A.C. / Pecorari, F. / Pluckthun, A. / Grutter, M.G. | ||||||
Citation | Journal: FEBS Lett. / Year: 2003 Title: Structural analysis of mycobacterial and murine hsp60 epitopes in complex with the class I MHC molecule H-2D(b) Authors: Ciatto, C. / Capitani, G. / Tissot, A.C. / Pecorari, F. / Plueckthun, A. / Gruetter, M.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n3n.cif.gz | 286.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n3n.ent.gz | 246.7 KB | Display | PDB format |
PDBx/mmJSON format | 1n3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/1n3n ftp://data.pdbj.org/pub/pdb/validation_reports/n3/1n3n | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
6 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly consists of one alpha chain, one beta-2 microglobulin chain, and a bound peptide antigen |
-Components
#1: Protein | Mass: 32470.111 Da / Num. of mol.: 4 / Fragment: EXTRACELLULAR DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01899 #2: Protein | Mass: 11704.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01887 #3: Protein/peptide | Mass: 945.029 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: SOLID-PHASE PEPTIDE SYNTHESIS #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 62.94 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonim sulfate, glycerol, tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.872 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 4, 2000 |
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.872 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. all: 47412 / Num. obs: 47412 / % possible obs: 99.9 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 3→3.11 Å / % possible all: 100 |
Reflection | *PLUS Highest resolution: 3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 100 % / Redundancy: 3.8 % / Num. unique obs: 4725 / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.5 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→30 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / % reflection Rfree: 3 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |