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Yorodumi- PDB-1ffp: CRYSTAL STRUCTURE OF MURINE CLASS I H-2DB COMPLEXED WITH PEPTIDE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ffp | ||||||
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Title | CRYSTAL STRUCTURE OF MURINE CLASS I H-2DB COMPLEXED WITH PEPTIDE GP33 (C9M/K1S) | ||||||
Components |
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Keywords | IMMUNE SYSTEM/SIGNALING PROTEIN / major histocompatibility complex / peptide binding / T cell receptor / IMMUNE SYSTEM-SIGNALING PROTEIN COMPLEX | ||||||
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 / Resolution: 2.6 Å | ||||||
Authors | Wang, B. / Sharma, A. / Maile, R. / Saad, M. / Collins, E.J. / Frelinger, J.A. | ||||||
Citation | Journal: J.IMMUNOL. / Year: 2002 Title: Peptidic termini play a significant role in TCR recognition Authors: Wang, B. / Sharma, A. / Maile, R. / Saad, M. / Collins, E.J. / Frelinger, J.A. #1: 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. / Apella, 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 | 1ffp.cif.gz | 157.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ffp.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ffp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/1ffp ftp://data.pdbj.org/pub/pdb/validation_reports/ff/1ffp | HTTPS FTP |
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-Related 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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Details | H-2Db heavy chain is noncovalently associated to Beat-2 microglobulin light chain. Heavy chain comprises of three subunits alpha1, alpha2 and alpha3. Peptide bind in the binding cleft formed by the alpha1 and alpha2 domains of heavy chain. |
-Components
#1: Protein | Mass: 31804.420 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR PORTION Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01899 #2: Protein | Mass: 11835.555 Da / Num. of mol.: 2 / Fragment: BETA-2 MICROGLOBULIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01887 #3: Protein/peptide | Mass: 1003.130 Da / Num. of mol.: 2 / Mutation: C9M/K1A / Source method: obtained synthetically / Details: The peptide was synthesized #4: Water | ChemComp-HOH / | |
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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: 2.49 Å3/Da / Density % sol: 50.67 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 8000, 6% DMSO, 0.8M Glycine, 150mM NaCl 25mM MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
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 IIC / Detector: IMAGE PLATE / Date: Sep 18, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 25600 / Num. obs: 25600 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.01 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.025 / Num. unique all: 4107 / % possible all: 95.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 109795 |
Reflection shell | *PLUS % possible obs: 95.2 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.48 |
-Processing
Software |
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Refinement | Resolution: 2.6→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 885473.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used Maximum Likelihood function
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.29 Å2 / ksol: 0.396 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PA / Topol file: PROTEIN.TOP | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.6 Å |