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- PDB-5e8p: The structure of the TEIPP associated altered peptide ligand Trh4... -
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Open data
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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) | ||||||
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![]() | IMMUNE SYSTEM / Cancer / Neo-epitope / TAP-deficiency / TEIPP / MHC-I / Sulfur-pi interactions / Non-classical peptide binding | ||||||
Function / homology | ![]() 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 / 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 / peptide binding / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / 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 / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / endoplasmic reticulum membrane / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / DNA binding / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hafstrand, I. / Doorduijn, E. / Duru, A.D. / Buratto, J. / Oliveira, C.C. / Sandalova, T. / van Hall, T. / Achour, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.2 KB | Display | ![]() |
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PDB format | ![]() | 136.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.9 KB | Display | ![]() |
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Full document | ![]() | 482.9 KB | Display | |
Data in XML | ![]() | 30.5 KB | Display | |
Data in CIF | ![]() | 43.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5e8nC ![]() 5e8oC ![]() 1s7uS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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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.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 11704.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein/peptide | Mass: 1038.371 Da / Num. of mol.: 2 / Fragment: UNP residues 379-387 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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