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Yorodumi- PDB-3ftg: Crystal Structure of H2Db in complex with NP366-N3A variant pepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ftg | ||||||
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Title | Crystal Structure of H2Db in complex with NP366-N3A variant peptide from influenza | ||||||
Components |
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Keywords | IMMUNE SYSTEM / H2Db / mouse MHC / influenza / immunology / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Immunoglobulin domain / Secreted | ||||||
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 / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Gras, S. / Guillonneau, C. / Rossjohn, J. | ||||||
Citation | Journal: Plos Pathog. / Year: 2010 Title: Protective efficacy of cross-reactive CD8+ T cells recognising mutant viral epitopes depends on peptide-MHC-I structural interactions and T cell activation threshold. Authors: Valkenburg, S.A. / Gras, S. / Guillonneau, C. / La Gruta, N.L. / Thomas, P.G. / Purcell, A.W. / Rossjohn, J. / Doherty, P.C. / Turner, S.J. / Kedzierska, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ftg.cif.gz | 89.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ftg.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ftg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ftg_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 3ftg_full_validation.pdf.gz | 450 KB | Display | |
Data in XML | 3ftg_validation.xml.gz | 16 KB | Display | |
Data in CIF | 3ftg_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/3ftg ftp://data.pdbj.org/pub/pdb/validation_reports/ft/3ftg | HTTPS FTP |
-Related structure data
Related structure data | 3cplS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32601.303 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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) / Gene: B2m / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887 |
#3: Protein/peptide | Mass: 983.074 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#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: 3.24 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M lithium sulfate, 28% PEG 3350, 0.1M sodium citrate, 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: Aug 14, 2007 / Details: MIRRORS |
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→20 Å / Num. obs: 18264 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.22 % / Biso Wilson estimate: 47.68 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.55 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 6.93 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 6.4 / Num. measured obs: 13218 / Num. unique all: 1905 / Num. unique obs: 1905 / % possible all: 97.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CPL Resolution: 2.6→15 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.839 / WRfactor Rfree: 0.282 / WRfactor Rwork: 0.202 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.814 / SU B: 22.366 / SU ML: 0.248 / SU R Cruickshank DPI: 0.52 / SU Rfree: 0.355 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.526 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.26 Å2 / Biso mean: 40.807 Å2 / Biso min: 9.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.665 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -25.9475 Å / Origin y: 2.5776 Å / Origin z: 21.4264 Å
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Refinement TLS group |
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