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- PDB-1n3n: Crystal structure of a mycobacterial hsp60 epitope with the murin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n3n | ||||||
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Title | Crystal structure of a mycobacterial hsp60 epitope with the murine class I MHC molecule H-2Db | ||||||
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![]() | IMMUNE SYSTEM / Immunoglobulin fold | ||||||
Function / homology | ![]() Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ciatto, C. / Capitani, G. / Tissot, A.C. / Pecorari, F. / Pluckthun, A. / Grutter, M.G. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 286.4 KB | Display | ![]() |
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PDB format | ![]() | 246.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 531 KB | Display | ![]() |
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Full document | ![]() | 614.8 KB | Display | |
Data in XML | ![]() | 66.9 KB | Display | |
Data in CIF | ![]() | 91.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Details | The biological assembly consists of one alpha chain, one beta-2 microglobulin chain, and a bound peptide antigen |
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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.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11704.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #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 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 62.94 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3 Å / % reflection Rfree: 3 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |