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Yorodumi- PDB-5e8p: The structure of the TEIPP associated altered peptide ligand Trh4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e8p | ||||||
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Title | The structure of the TEIPP associated altered peptide ligand Trh4-p5NLE in complex with H-2D(b) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Cancer / Neo-epitope / TAP-deficiency / TEIPP / MHC-I / Sulfur-pi interactions / Non-classical peptide binding | ||||||
Function / homology | Function and homology information sphingosine N-acyltransferase / sphingoid base N-palmitoyltransferase / Sphingolipid de novo biosynthesis / sphingosine N-acyltransferase activity / sphingolipid biosynthetic process / ceramide biosynthetic process / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway ...sphingosine N-acyltransferase / sphingoid base N-palmitoyltransferase / Sphingolipid de novo biosynthesis / sphingosine N-acyltransferase activity / sphingolipid biosynthetic process / ceramide biosynthetic process / 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 / endoplasmic reticulum membrane / protein-containing complex binding / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / DNA binding / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hafstrand, I. / Doorduijn, E. / Duru, A.D. / Buratto, J. / Oliveira, C.C. / Sandalova, T. / van Hall, T. / Achour, A. | ||||||
Citation | Journal: J Immunol. / Year: 2016 Title: The MHC Class I Cancer-Associated Neoepitope Trh4 Linked with Impaired Peptide Processing Induces a Unique Noncanonical TCR Conformer. Authors: Hafstrand, I. / Doorduijn, E.M. / Duru, A.D. / Buratto, J. / Oliveira, C.C. / Sandalova, T. / van Hall, T. / Achour, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e8p.cif.gz | 172.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e8p.ent.gz | 136.7 KB | Display | PDB format |
PDBx/mmJSON format | 5e8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e8p_validation.pdf.gz | 474.9 KB | Display | wwPDB validaton report |
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Full document | 5e8p_full_validation.pdf.gz | 482.9 KB | Display | |
Data in XML | 5e8p_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 5e8p_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/5e8p ftp://data.pdbj.org/pub/pdb/validation_reports/e8/5e8p | HTTPS FTP |
-Related structure data
Related structure data | 5e8nC 5e8oC 1s7uS 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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Unit cell |
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-Components
#1: Protein | Mass: 32087.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899 #2: Protein | Mass: 11704.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887 #3: Protein/peptide | Mass: 1038.371 Da / Num. of mol.: 2 / Fragment: UNP residues 379-387 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9D6K9, sphingosine N-acyltransferase #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.6 M ammonium sulphate, 0.1 M Tris-HCl, 0.5 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.965 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2013 / Details: ID30A-1/MASSIF-1, PILATUS3 2M |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 2→32.3 Å / Num. obs: 68583 / % possible obs: 96.5 % / Observed criterion σ(I): 4.2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S7U Resolution: 2→31.802 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→31.802 Å
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Refine LS restraints |
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LS refinement shell |
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