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Yorodumi- PDB-1yn6: Crystal structure of a mouse MHC class I protein, H2-Db, in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yn6 | ||||||
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Title | Crystal structure of a mouse MHC class I protein, H2-Db, in complex with a peptide from the influenza A acid polymerase | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC class 1 / H2-Db / influenza A / peptide of acid polymerase | ||||||
Function / homology | Function and homology information 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 / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...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 / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 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 / cap snatching / peptide binding / 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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / 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 / endonuclease activity / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / learning or memory / Hydrolases; Acting on ester bonds / immune response / external side of plasma membrane / lysosomal membrane / viral RNA genome replication / signaling receptor binding / DNA-templated transcription / host cell nucleus / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Turner, S.J. / Kedzierska, K. / Komodromou, H. / La Gruta, N.L. / Dunstone, M.A. / Webb, A.I. / Webby, R. / Walden, H. / Xie, W. / McCluskey, J. ...Turner, S.J. / Kedzierska, K. / Komodromou, H. / La Gruta, N.L. / Dunstone, M.A. / Webb, A.I. / Webby, R. / Walden, H. / Xie, W. / McCluskey, J. / Purcell, A.W. / Rossjohn, J. / Doherty, P.C. | ||||||
Citation | Journal: Nat.Immunol. / Year: 2005 Title: Lack of prominent peptide-major histocompatibility complex features limits repertoire diversity in virus-specific CD8+ T cell populations Authors: Turner, S.J. / Kedzierska, K. / Komodromou, H. / La Gruta, N.L. / Dunstone, M.A. / Webb, A.I. / Webby, R. / Walden, H. / Xie, W. / McCluskey, J. / Purcell, A.W. / Rossjohn, J. / Doherty, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yn6.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yn6.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 1yn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yn6_validation.pdf.gz | 377.1 KB | Display | wwPDB validaton report |
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Full document | 1yn6_full_validation.pdf.gz | 387.6 KB | Display | |
Data in XML | 1yn6_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 1yn6_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/1yn6 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/1yn6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31804.420 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): XLBlue / References: UniProt: P01899 |
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#2: Protein | Mass: 11835.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): XLBlue / References: UniProt: P01887 |
#3: Protein/peptide | Mass: 1186.295 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic peptide with same sequence as influenza A acid polymerase fragment, residues 224-233 References: UniProt: P13175, RNA-directed RNA polymerase |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: sodium citrate, ammonium acetate, PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 30, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. all: 31028 / Num. obs: 28360 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 2→2.2 Å / % possible all: 43.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→100 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→100 Å
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Refine LS restraints |
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