+Open data
-Basic information
Entry | Database: PDB / ID: 1kbg | |||||||||
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Title | MHC Class I H-2KB Presented Glycopeptide RGY8-6H-GAL2 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC / MAJOR HISTOCOMPATIBILITY COMPLEX / ANTIGEN PRESENTATION / GLYCOPEPTIDE / CELLULAR IMMUNITY / IMMUNOLOGY / CELL SURFACE RECEPTOR / SYNTHETIC PEPTIDE / VACCINE | |||||||||
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 / helical viral capsid / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / inner ear development / 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 / 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 / positive regulation of type II interferon production / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / viral nucleocapsid / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / host cell cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / molecular replacement / Resolution: 2.2 Å | |||||||||
Authors | Speir, J.A. / Abdel-Motal, U.M. / Jondal, M. / Wilson, I.A. | |||||||||
Citation | Journal: Immunity / Year: 1999 Title: Crystal structure of an MHC class I presented glycopeptide that generates carbohydrate-specific CTL. Authors: Speir, J.A. / Abdel-Motal, U.M. / Jondal, M. / Wilson, I.A. #1: Journal: Eur.J.Immunol. / Year: 1996 Title: Immunization with Glycosylated Kb-Binding Peptides Generates Carbohydrate- Specific, Unrestricted Cytotoxic T Cells Authors: Abdel-Motal, U.M. / Berg, L. / Rosen, A. / Bengtsson, M. / Thorpe, C.J. / Kihlberg, J. / Dahmen, J. / Magnusson, G. / Karlsson, K. / Jondal, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kbg.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kbg.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/1kbg ftp://data.pdbj.org/pub/pdb/validation_reports/kb/1kbg | HTTPS FTP |
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-Related structure data
Related structure data | 2vaaS 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 HL
#1: Protein | Mass: 31648.322 Da / Num. of mol.: 1 / Fragment: PEPTIDE-BINDING DOMAIN Source method: isolated from a genetically manipulated source Details: FORMS HETERODIMER WITH CHAIN L, AND THEN A TRIMOLECULAR COMPLEX WITH CHAIN P Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/B / Description: TRUNCATED AFTER RESIDUE 274 / Cell: MOST NUCLEATED CELLS / Cellular location: CYTOPLASM, ER, CELL SURFACE / Cellular location (production host): SECRETED / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01901 |
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#2: Protein | Mass: 11704.359 Da / Num. of mol.: 1 / Fragment: MHC ASSOCIATED LIGHT CHAIN / Source method: isolated from a natural source / Details: TRUNCATED AFTER RESIDUE 99 / Source: (natural) Mus musculus (house mouse) / Cell: MOST NUCLEATED CELLS / Cellular location: CYTOPLASM, ER, CELL SURFACE / Strain: BALB/B / References: UniProt: P01887 |
-Protein/peptide / Non-polymers , 2 types, 109 molecules P
#3: Protein/peptide | Mass: 973.172 Da / Num. of mol.: 1 / Fragment: H-2KB-BOUND GLYCOPEPTIDE / Source method: obtained synthetically Details: VSV NUCLEOPROTEIN RESIDUES 52-59 COMMONLY REFERRED TO AS VSV-8 FROM THE VESICULAR STOMATITIS VIRUS. RESIDUE 57 IS REPLACED BY A SYNTHETIC GLYCOSYLATED AMINO ACID. References: UniProt: P11212 |
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#7: Water | ChemComp-HOH / |
-Sugars , 3 types, 3 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[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: Polysaccharide | alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||
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Crystal grow | pH: 6.4 / Details: 2.3M Na/K PHOSPHATE, 2% MPD, pH 6.4 | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 133 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996 / Details: DOUBLE-FOCUSING MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 28511 / % possible obs: 89.3 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 34.8 Å2 / Rsym value: 0.078 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.384 / % possible all: 55 |
Reflection | *PLUS Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 55 % / Num. unique obs: 1734 / Rmerge(I) obs: 0.384 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB ENTRY 2VAA Resolution: 2.2→18 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: SOME PARAMETER/TOPOLOGY LIBRARIES HAVE BEEN MODIFIED IN-HOUSE TO PROVIDE MISSING OR CORRECTED SPECIFICATIONS FOR CARBOHYDRATE AND/OR PROTEIN.
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Displacement parameters | Biso mean: 30.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 18 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.424 / % reflection Rfree: 10 % / Rfactor Rwork: 0.368 |