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Yorodumi- PDB-1bz9: CRYSTAL STRUCTURE OF MURINE CLASS I MHC H2-DB COMPLEXED WITH A SY... -
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-Basic information
Entry | Database: PDB / ID: 1bz9 | |||||||||
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Title | CRYSTAL STRUCTURE OF MURINE CLASS I MHC H2-DB COMPLEXED WITH A SYNTHETIC PEPTIDE P1027 | |||||||||
Components |
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Keywords | MURINE CLASS I MHC/PEPTIDE COMPLEX / MURINE CLASS I MHC-PEPTIDE COMPLEX / MURINE CLASS I MHC-PEPTIDE COMPLEX complex | |||||||||
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 / 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 / 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 / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / external side of plasma membrane / lysosomal 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 | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Zhao, R. / Collins, E.J. | |||||||||
Citation | Journal: J.Exp.Med. / Year: 1999 Title: Structural evidence of T cell xeno-reactivity in the absence of molecular mimicry. Authors: Zhao, R. / Loftus, D.J. / Appella, E. / Collins, E.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bz9.cif.gz | 90.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bz9.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 1bz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bz9_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 1bz9_full_validation.pdf.gz | 447.5 KB | Display | |
Data in XML | 1bz9_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 1bz9_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/1bz9 ftp://data.pdbj.org/pub/pdb/validation_reports/bz/1bz9 | HTTPS FTP |
-Related structure data
Related structure data | 1b0gC 1hocS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32406.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: FOLDED WITH SYNTHETIC PEPTIDE IN VITRO / Cellular location: CELL SURFACE / Plasmid: PLM1 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / 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) / Description: FOLDED WITH SYNTHETIC PEPTIDE IN VITRO / Cellular location: CELL SURFACE / Plasmid: PLM1 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS / References: UniProt: P01887 |
#3: Protein/peptide | Mass: 1028.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic |
#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: 2.7 Å3/Da / Density % sol: 54.02 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 11820 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 46.4 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 5.9 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 62278 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HOC Resolution: 2.8→30 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.48
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Displacement parameters | Biso mean: 34.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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