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Yorodumi- PDB-3tbs: CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY ... -
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-Basic information
Entry | Database: PDB / ID: 3tbs | ||||||
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Title | CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX THE WITH LCMV-DERIVED GP33 ALTERED PEPTIDE ligand (V3P,Y4A) | ||||||
Components |
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Keywords | Immune system/agonist / Murine MHC / LCMV / receptor binding / Beta2-microglobulin / Immune system / T cell recognition / antigen presentation / altered peptide ligand / agonism / antagonism / T cell receptor / CD8 / Cell Surface / Immune system-agonist complex | ||||||
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 / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / host cell Golgi membrane / 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 / peptide antigen assembly with MHC class I protein complex / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / 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 / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Lymphocytic choriomeningitis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Duru, A.D. / Allerbring, E.B. / Uchtenhagen, H. / Mazumdar, P.A. / Badia-Martinez, D. / Madhurantakam, C. / Sandalova, T. / Nygren, P. / Achour, A. | ||||||
Citation | Journal: To be Published Title: Conversion of a T cell viral antagonist into an agonist through higher stabilization and conserved molecular mimicry: Implications for TCR recognition Authors: Duru, A.D. / Allerbring, E.B. / Uchtenhagen, H. / Mazumdar, P.A. / Badia-Martinez, D. / Madhurantakam, C. / Sandalova, T. / Nygren, P. / Achour, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tbs.cif.gz | 322.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tbs.ent.gz | 264.9 KB | Display | PDB format |
PDBx/mmJSON format | 3tbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/3tbs ftp://data.pdbj.org/pub/pdb/validation_reports/tb/3tbs | HTTPS FTP |
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-Related structure data
Related structure data | 3tbtC 3tbvC 3tbwC 3tbyC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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-Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 32087.703 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1, H2-DB / Plasmid: Pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899 #2: Protein | Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: Pet3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887 |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 951.120 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 33-41 / Mutation: V35P,Y36A / Source method: obtained synthetically / Details: LYMPHOCYTIC CHORIOMENINGITIS VIRUS / Source: (synth.) Lymphocytic choriomeningitis virus / References: UniProt: P07399 |
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-Non-polymers , 3 types, 151 molecules
#4: Chemical | #5: Chemical | #6: 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: 3.32 Å3/Da / Density % sol: 62.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Crystals were obtained in 1.6-1.8 M ammonium sulfate, 0.1 M Tris HCl pH 7.0-9.0 screening conditions. 4 ul of a 5mg/ml protein solution were mixed in a 4:2 ratio with the crystallization ...Details: Crystals were obtained in 1.6-1.8 M ammonium sulfate, 0.1 M Tris HCl pH 7.0-9.0 screening conditions. 4 ul of a 5mg/ml protein solution were mixed in a 4:2 ratio with the crystallization reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2008 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→49.21 Å / Num. all: 40587 / Num. obs: 40587 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5927 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S7U Resolution: 2.49→49.21 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.88 / SU B: 23.066 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R Free: 0.28 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.417 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→49.21 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.487→2.551 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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