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Yorodumi- PDB-2ve6: Crystal structure of a Murine MHC class I H2-Db molecule in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ve6 | |||||||||
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Title | Crystal structure of a Murine MHC class I H2-Db molecule in complex with a photocleavable peptide | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / PHOTOCLEAVABLE PEPTIDE / AUXILIARY ANCHORING RESIDUE / GLYCOPROTEIN / TRANSMEMBRANE / PEPTIDE LOADING / IMMUNE RESPONSE / IMMUNOGLOBULIN DOMAIN / MHC / SEV9 / MHC I / MEMBRANE / SECRETED | |||||||||
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 / 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 / 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 / adaptive immune response / learning or memory Similarity search - Function | |||||||||
Biological species | MUS MUSCULUS (house mouse) SENDAI VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Grotenbreg, G.M. / Roan, N.R. / Guillen, E. / Meijers, R. / Wang, J.H. / Bell, G.W. / Starnbach, M.N. / Ploegh, H.L. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Discovery of Cd8+ T Cell Epitopes in Chlamydia Trachomatis Infection Through Use of Caged Class I Mhc Tetramers. Authors: Grotenbreg, G.M. / Roan, N.R. / Guillen, E. / Meijers, R. / Wang, J.H. / Bell, G.W. / Starnbach, M.N. / Ploegh, H.L. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ve6.cif.gz | 315.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ve6.ent.gz | 258.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ve6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/2ve6 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/2ve6 | HTTPS FTP |
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-Related structure data
Related structure data | 1wbxS S: Starting model for refinement |
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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 / Refine code: 5
NCS ensembles :
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-Components
#1: Protein | Mass: 32184.816 Da / Num. of mol.: 4 / Fragment: RESIDUES 25-301 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: BL21 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01899 #2: Protein | Mass: 11678.388 Da / Num. of mol.: 4 / Fragment: RESIDUES 22-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: BL21 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01887 #3: Protein/peptide | Mass: 1044.117 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: 3-AMINO-3-(2-NITRO)PHENYL-PROPIONIC ACID AT P7 / Source: (synth.) SENDAI VIRUS #4: Water | ChemComp-HOH / | Nonpolymer details | 3-AMINO-3-(2-NITRO)PHENYL-PROPIONIC ACID (PRQ): PHOTOCLEAV | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING-DROP, VAPOR-DIFFUSION METHOD WITH A WELL SOLUTION OF 15% (W/V) PEG 8000, 0.05 M K/NA PHOSPHATE, 50-100 MM BETA-OCTYL-GLUCOPYRANOSIDE ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE USING THE HANGING-DROP, VAPOR-DIFFUSION METHOD WITH A WELL SOLUTION OF 15% (W/V) PEG 8000, 0.05 M K/NA PHOSPHATE, 50-100 MM BETA-OCTYL-GLUCOPYRANOSIDE AND 0.1 M CACODYLATE AT PH 6.4. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.07 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→20 Å / Num. obs: 50561 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WBX Resolution: 2.65→19.66 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.873 / SU B: 34.083 / SU ML: 0.345 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / 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: 47.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→19.66 Å
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Refine LS restraints |
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