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Yorodumi- PDB-2fo4: Enhanced MHC class I binding and immune responses through anchor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fo4 | |||||||||
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Title | Enhanced MHC class I binding and immune responses through anchor modification of the non-canonical tumor associated MUC1-8 peptide | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / anchor modifications / H-2Kb / MUC1 / non-canonical peptide / MUC1-8 / vaccine design | |||||||||
Function / homology | Function and homology information Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / 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 / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of membrane depolarization / Dectin-2 family / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / DNA damage response, signal transduction by p53 class mediator / localization / cellular defense response / beta-2-microglobulin binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / 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 / transcription coregulator activity / 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 / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / Golgi lumen / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / positive regulation of T cell activation / p53 binding / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / iron ion transport / protein refolding / antibacterial humoral response / protein homotetramerization / Interleukin-4 and Interleukin-13 signaling / intracellular iron ion homeostasis / vesicle / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / membrane => GO:0016020 / learning or memory / defense response to Gram-positive bacterium / defense response to bacterium / immune response / apical plasma membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / chromatin / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Lazoura, E. / Ramsland, P.A. | |||||||||
Citation | Journal: Immunology / Year: 2006 Title: Enhanced major histocompatibility complex class I binding and immune responses through anchor modification of the non-canonical tumour-associated mucin 1-8 peptide Authors: Lazoura, E. / Lodding, J. / Farrugia, W. / Ramsland, P.A. / Stevens, J. / Wilson, I.A. / Pietersz, G.A. / Apostolopoulos, V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fo4.cif.gz | 96.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fo4.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 2fo4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/2fo4 ftp://data.pdbj.org/pub/pdb/validation_reports/fo/2fo4 | HTTPS FTP |
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-Related structure data
Related structure data | 1g7qS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31648.322 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 1-274 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pRMHa-3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 cells / References: UniProt: P01901, UniProt: Q3UBW0*PLUS |
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#2: Protein | Mass: 11704.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pRMHa-3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 cells / References: UniProt: P01887 |
-Protein/peptide , 1 types, 1 molecules P
#3: Protein/peptide | Mass: 903.014 Da / Num. of mol.: 1 / Mutation: T5F, A8L / Source method: obtained synthetically Details: The 8-residue peptide of mucin 1 was chemically synthesized. References: UniProt: Q16615, UniProt: P15941*PLUS |
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-Sugars , 2 types, 2 molecules
#4: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 109 molecules
#6: Chemical | #7: Chemical | ChemComp-MPD / ( #8: 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: 3.03 Å3/Da / Density % sol: 59.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 1.9M sodium/potasium phosphate, 2% MPD, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-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: Feb 17, 2005 / 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: 2.7→50 Å / Num. all: 14860 / Num. obs: 14860 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1448 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G7Q Resolution: 2.7→41.8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 37.5 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→41.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.026
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