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Yorodumi- PDB-2ve6: Crystal structure of a Murine MHC class I H2-Db molecule in compl... -
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Open data
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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 informationEndosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / DAP12 signaling / cellular response to iron(III) ion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class Ib protein complex / response to molecule of bacterial origin ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / DAP12 signaling / cellular response to iron(III) ion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class Ib protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / multicellular organismal-level iron ion homeostasis / regulation of membrane depolarization / T cell differentiation in thymus / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response / Neutrophil degranulation / positive regulation of T cell mediated cytotoxicity / negative regulation of neuron projection development / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / protein refolding / MHC class I protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / late endosome membrane / cellular response to lipopolysaccharide / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-negative bacterium / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / innate immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / : / identical protein binding / plasma membrane / cytosol Similarity search - Function | |||||||||
| Biological species | ![]() 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: 2008Title: 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. |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2ve6.cif.gz | 315.5 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 |
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Links
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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.) ![]() ![]() #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.) ![]() ![]() #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 / | Has protein modification | Y | 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 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting 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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SENDAI VIRUS
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